fix(export): @vocab mints into the shipped ns# namespace (#1236)

fix(export): keep caller data out of the shipped ns# namespace

Every JSON-LD context set @vocab to https://semantica.dev/vocab/,
which 404s, so every bare term in caller data (extracted entity/
relationship types, arbitrary metadata keys) minted under a namespace
the package never ships. The obvious fix, pointing @vocab at
SEMANTICA_NS instead, turned out to be worse than the dead link: since
that namespace is real and populated, every bare term a caller happens
to use now expands into something that looks like official Semantica
vocabulary. An extracted type "ORG" became ns#ORG, a class the
vocabulary never defines. A metadata key "source" attached a plain
string value to sem:source, an owl:ObjectProperty that already exists
in semantica-ns.ttl with a resource-valued range, silently corrupting
its semantics.

@vocab is now removed from all five contexts (four in
json_exporter.py, one in rdf_exporter.py) rather than repointed.
Every document already used explicit semantica: prefixes for its own
terms, so nothing else in the output changes; an unscoped bare term
now simply fails to expand, which is standard JSON-LD behavior for a
context that doesn't know it, instead of being silently claimed by
our namespace.

Two call sites needed to stop handing caller data to @type/bare terms
in the first place:

- Entity nodes are always typed semantica:Entity now, with the
  caller's label carried as a semantica:type string instead of
  minted into @type. This matches how relationship nodes already
  carried their type. sem:type's domain in semantica-ns.ttl opens up
  to cover entities as well as relationships, following the
  sem:confidence precedent, since the property is now legitimately
  emitted for both.
- semantica:metadata gets an explicit @json term definition, so a
  caller's metadata dict travels as one rdf:JSON literal instead of
  having its keys expand as separate predicates. A metadata key can
  no longer collide with a real ontology term no matter what the
  caller names it.

Both JSONExporter and RDFExporter.serialize_to_jsonld got the same
treatment, since they build separate JSON-LD structures for the same
underlying data.

The regression tests assert the negative space this bug lived in: no
context declares @vocab, no caller type label appears as an rdf:type
under ns#, and no caller metadata key appears as a predicate under
ns# at all, only as content inside the single JSON literal.

Closes #1146

.github/DISCUSSION_TEMPLATE/ideas.md

@@ -69,5 +69,5 @@ If you have ideas on how this could be implemented, please share.
 
 ---
 
-**Note**: For feature requests that are ready to be implemented, consider creating a [Feature Request issue](https://github.com/Hawksight-AI/semantica/issues/new?template=feature_request.md) instead.
+**Note**: For feature requests that are ready to be implemented, consider creating a [Feature Request issue](https://github.com/semantica-agi/semantica/issues/new?template=feature_request.md) instead.
 

.github/DISCUSSION_TEMPLATE/qa.md

@@ -46,8 +46,8 @@ If applicable, paste any error messages or describe unexpected behavior:
 
 ## Checklist
 
-- [ ] I have searched existing [discussions](https://github.com/Hawksight-AI/semantica/discussions) and [issues](https://github.com/Hawksight-AI/semantica/issues)
-- [ ] I have checked the [documentation](https://github.com/Hawksight-AI/semantica/tree/main/docs) and [FAQ](https://github.com/Hawksight-AI/semantica/blob/main/docs/faq.md)
+- [ ] I have searched existing [discussions](https://github.com/semantica-agi/semantica/discussions) and [issues](https://github.com/semantica-agi/semantica/issues)
+- [ ] I have checked the [documentation](https://github.com/semantica-agi/semantica/tree/main/docs) and [FAQ](https://github.com/semantica-agi/semantica/blob/main/docs/faq.md)
 - [ ] I have provided a minimal code example (if applicable)
 - [ ] I have included error messages (if applicable)
 - [ ] I have provided environment details

.github/FUNDING.yml

@@ -1,3 +1,3 @@
 # Funding options for Semantica
-github: Hawksight-AI
+github: semantica-agi
 

.github/ISSUE_TEMPLATE/config.yml

@@ -1,8 +1,8 @@
 blank_issues_enabled: true
 contact_links:
   - name: 📚 Documentation
-    url: https://github.com/Hawksight-AI/semantica/tree/main/docs
+    url: https://github.com/semantica-agi/semantica/tree/main/docs
     about: Browse the documentation
   - name: 💬 Discussions
-    url: https://github.com/Hawksight-AI/semantica/discussions
+    url: https://github.com/semantica-agi/semantica/discussions
     about: Ask questions and discuss with the community

.github/SUPPORT.md

@@ -3,31 +3,31 @@
 ## Getting Help
 
 ### 📚 Documentation
-Check the [docs folder](https://github.com/Hawksight-AI/semantica/tree/main/docs) and [README](https://github.com/Hawksight-AI/semantica/blob/main/README.md) for guides and examples.
+Check the [docs folder](https://github.com/semantica-agi/semantica/tree/main/docs) and [README](https://github.com/semantica-agi/semantica/blob/main/README.md) for guides and examples.
 
 ### 💬 Community Support
-- **GitHub Discussions**: [Ask questions](https://github.com/Hawksight-AI/semantica/discussions)
+- **GitHub Discussions**: [Ask questions](https://github.com/semantica-agi/semantica/discussions)
 - **Discord**: Join our [Discord server](https://discord.gg/sV34vps5hH) for real-time chat
 
 ### 💭 Discussions
-Join the conversation on [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions):
+Join the conversation on [GitHub Discussions](https://github.com/semantica-agi/semantica/discussions):
 - **Q&A**: Ask questions and get help from the community
 - **Ideas**: Share feature requests and suggestions
 - **Show and Tell**: Showcase your projects and use cases
 - **General**: General discussions about Semantica
 
 ### 🐛 Bug Reports
-Found a bug? [Create an issue](https://github.com/Hawksight-AI/semantica/issues/new/choose)
+Found a bug? [Create an issue](https://github.com/semantica-agi/semantica/issues/new/choose)
 
 ### 📖 Resources
-- [Quick Start Guide](https://github.com/Hawksight-AI/semantica/blob/main/docs/quickstart.md)
-- [FAQ](https://github.com/Hawksight-AI/semantica/blob/main/docs/faq.md)
-- [Cookbook Examples](https://github.com/Hawksight-AI/semantica/tree/main/cookbook)
+- [Quick Start Guide](https://github.com/semantica-agi/semantica/blob/main/docs/quickstart.md)
+- [FAQ](https://github.com/semantica-agi/semantica/blob/main/docs/faq.md)
+- [Cookbook Examples](https://github.com/semantica-agi/semantica/tree/main/cookbook)
 
 ## Commercial Support
 
 For enterprise support, custom development, or consulting services:
-- Contact us through [GitHub Issues](https://github.com/Hawksight-AI/semantica/issues)
+- Contact us through [GitHub Issues](https://github.com/semantica-agi/semantica/issues)
 - Include "Commercial Support" in the title
 
 ## Sponsorship
@@ -35,7 +35,7 @@ For enterprise support, custom development, or consulting services:
 ### Sponsor this project
 
 Support Semantica development:
-- [GitHub Sponsors](https://github.com/sponsors/Hawksight-AI)
+- [GitHub Sponsors](https://github.com/sponsors/semantica-agi)
 
 Your sponsorship helps us:
 - Maintain and improve the framework

.github/pull_request_template.md

@@ -1,4 +1,4 @@
-> **Before you submit:** make sure you followed the [issue workflow in CONTRIBUTING.md](https://github.com/semantica-agi/semantica/blob/main/CONTRIBUTING.md#-working-on-an-existing-issue) — comment on the issue and wait for assignment before opening a PR, to avoid duplicate work.
+> **Before you submit:** make sure you followed the [issue workflow in CONTRIBUTING.md](https://github.com/semantica-agi/semantica/blob/main/CONTRIBUTING.md#-working-on-an-existing-issue) — wait for the issue to be assigned to you before opening a PR, to avoid duplicate work.
 
 ## Description
 

.github/workflows/benchmark.yml

@@ -17,10 +17,10 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.11
         uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
-          python-version: "3.12"
+          python-version: "3.11"
           cache: 'pip'
 
       - name: Install Dependencies

.github/workflows/ci.yml

@@ -42,8 +42,28 @@ jobs:
       - name: Build Explorer frontend
         working-directory: explorer
         run: npm run build
+      - name: Install pinned Python dependencies
+        run: |
+          pip install -r requirements-ci.txt
+      - name: Verify requirements-ci.txt is up to date
+        run: |
+          pip install uv==0.12.1
+          # Re-resolve with the committed file as a constraint: upstream package
+          # releases must NOT fail CI (deps only change when pyproject.toml
+          # changes intentionally). Compare only version lines (pkg==ver),
+          # ignoring the -c constraint comments and the `\` line continuations
+          # that --generate-hashes emits.
+          uv pip compile pyproject.toml --python-version 3.11 --extra all \
+            --constraint requirements-ci.txt -o /tmp/requirements-ci-check.txt
+          diff \
+            <(grep -E '^[a-zA-Z0-9._-]+==' requirements-ci.txt | sed 's/ \\$//') \
+            <(grep -E '^[a-zA-Z0-9._-]+==' /tmp/requirements-ci-check.txt)
       - run: pip install build
-      - run: python -m build
+      # wheel is build-time only (not in requirements-ci.txt) — install the
+      # same pinned version [build-system] declares so --no-isolation works.
+      - run: pip install wheel==0.48.0
+      - name: Build package (no isolation — pinned deps)
+        run: python -m build --no-isolation
       - name: Verify Explorer frontend is packaged
         run: |
           python - <<'PY'

.github/workflows/codeql.yml

@@ -32,7 +32,7 @@ jobs:
       # meaningful state carried over from a failed attempt.
       - name: Initialize CodeQL (attempt 1)
         id: codeql-init-1
-        uses: github/codeql-action/init@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+        uses: github/codeql-action/init@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
         continue-on-error: true
         with:
           languages: python
@@ -42,7 +42,7 @@ jobs:
       - name: Initialize CodeQL (attempt 2)
         id: codeql-init-2
         if: steps.codeql-init-1.outcome == 'failure'
-        uses: github/codeql-action/init@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+        uses: github/codeql-action/init@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
         continue-on-error: true
         with:
           languages: python
@@ -52,17 +52,17 @@ jobs:
       - name: Initialize CodeQL (attempt 3)
         id: codeql-init-3
         if: steps.codeql-init-2.outcome == 'failure'
-        uses: github/codeql-action/init@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+        uses: github/codeql-action/init@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
         with:
           languages: python
           queries: security-and-quality
           config-file: .github/codeql/codeql-config.yml
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+        uses: github/codeql-action/autobuild@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+        uses: github/codeql-action/analyze@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
         with:
           category: "/language:python"
           upload: false
@@ -72,7 +72,7 @@ jobs:
         # Uploads results only when Default Setup is not active.
         # If Default Setup is still enabled, this step skips gracefully
         # instead of failing the workflow with HTTP 409.
-        uses: github/codeql-action/upload-sarif@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+        uses: github/codeql-action/upload-sarif@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
         with:
           sarif_file: ${{ steps.codeql.outputs.sarif-output }}
           category: "/language:python"

.github/workflows/defender-for-devops.yml

@@ -57,7 +57,7 @@ jobs:
         # avoiding the guardian.cmd/checkov exit-code bug in the MSDO wrapper.
         tools: eslint,templateanalyzer,terrascan
     - name: Upload results to Security tab
-      uses: github/codeql-action/upload-sarif@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+      uses: github/codeql-action/upload-sarif@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
       with:
         sarif_file: ${{ steps.msdo.outputs.sarifFile }}
 
@@ -82,7 +82,7 @@ jobs:
         }
 
     - name: Upload Checkov results to Security tab
-      uses: github/codeql-action/upload-sarif@5595ccaf912efad79be6eef63a5619ff05969be3 # v4
+      uses: github/codeql-action/upload-sarif@ff2f1c621b7f889edc0d3c761ac2e6a3f8cdb0dd # v4
       if: always()
       with:
         sarif_file: reports/checkov.sarif

.github/workflows/release.yml

@@ -36,8 +36,16 @@ jobs:
         run: |
           npm ci
           npm run build
+      # Install the pinned dependency set (with hashes) so the sdist/wheel
+      # build runs against the same versions CI tests against.
+      - name: Install pinned build dependencies
+        run: pip install -r requirements-ci.txt
       - run: pip install build
-      - run: python -m build
+      # wheel is build-time only (not in requirements-ci.txt) — install the
+      # same pinned version [build-system] declares so --no-isolation works.
+      - run: pip install wheel==0.48.0
+      - name: Build package (no isolation — pinned deps)
+        run: python -m build --no-isolation
       - name: Verify Explorer frontend is packaged
         run: |
           python - <<'PY'

.github/workflows/security-scan.yml

@@ -45,11 +45,14 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          # Install the pinned dependency set FIRST so Safety scans Semantica's
+          # exact CI/release dependency tree (requirements-ci.txt is generated
+          # from pyproject.toml extras, so this covers the project's real deps).
+          pip install -r requirements-ci.txt
+          # Tooling AFTER the pinned set: installing safety/bandit/semgrep/jq
+          # first lets the pinned requirements overwrite their transitive deps
+          # (e.g. rich), which breaks the safety CLI at runtime.
           pip install safety bandit semgrep jq
-          # Install the project itself (core deps + the LiteLLM provider extra)
-          # so Safety scans Semantica's actual dependency tree, not just the
-          # scanner tools' own dependencies.
-          pip install -e ".[llm-litellm]"
 
       - name: Run Safety Check (Package Vulnerabilities)
         run: |

.github/workflows/security.yml

@@ -4,6 +4,12 @@ on:
   schedule:
     - cron: '0 0 * * 1'
   workflow_dispatch:
+  pull_request:
+    branches: [main]
+    paths:
+      - 'pyproject.toml'
+      - 'requirements-ci.txt'
+      - '.github/workflows/security.yml'
 
 permissions:
   contents: read
@@ -16,6 +22,21 @@ jobs:
       - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: '3.11'
+      # Upgrade first: actions/setup-python's baked-in setuptools has been
+      # behind known-vulnerable floors before (e.g. PYSEC-2026-3447 /
+      # setuptools 75.1.0), so don't trust the preinstalled one.
+      - run: python -m pip install --upgrade pip setuptools
+      # Audit the pinned dependency set (requirements-ci.txt is compiled from
+      # pyproject.toml with --extra all — the same coverage as the [all]
+      # extra, minus the Linux-only gpu set — so this keeps scan parity with
+      # CI/release builds without a time-dependent resolution). This is the
+      # fix for PYSEC-2024-38 (#869): the bare-env job never had fastapi or
+      # python-multipart installed to look at.
+      - run: pip install -r requirements-ci.txt
+      # PR runs gate on findings, since they're scoped to actual
+      # pyproject.toml changes under review. The schedule/workflow_dispatch
+      # runs stay non-blocking until a full pass over pre-existing findings
+      # across the whole [all] tree has been done.
       - run: pip install pip-audit
-      - run: pip-audit
-        continue-on-error: true
+      - run: pip-audit -r requirements-ci.txt
+        continue-on-error: ${{ github.event_name != 'pull_request' }}

CHANGELOG.md

@@ -9,6 +9,454 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.6.7] - 2026-08-28
+
+### Added
+
+- **First-class LangChain integration** (closes #963; recreates #969)
+  - New `pip install semantica[langchain]` extra (`langchain-core>=0.3.0`), included in the `all` bundle
+  - `integrations/langchain/SemanticaRetriever` — LangChain `BaseRetriever` that seeds from `HybridSearch` then walks graph edges (`hops=2` default) for GraphRAG-style retrieval; falls back to `ContextGraph.query` when hybrid search is unavailable
+  - `integrations/langchain/SemanticaVectorStore` — LangChain `VectorStore` adapter over `HybridSearch` (`add_texts`, `similarity_search`, `similarity_search_with_score`, `from_texts`)
+  - `integrations/langchain/SemanticaKGTool` / `SemanticaDecisionTool` — `BaseTool` subclasses with Pydantic `args_schema` (`semantica_query_graph`, `semantica_query_decisions`); `build()` returns the tool, or `None` when langchain-core is absent
+  - Retriever and VectorStore read HybridSearch nested `metadata` (`content`, `node_id`, `node_type`) rather than top-level fields that HybridSearch does not set
+  - All adapters remain importable without langchain-core (`LANGCHAIN_AVAILABLE` flag)
+  - Docs: `docs/integrations/langchain.md`, README native-integration matrix, and `docs.json` nav entry
+
+- **SAP OData ingestor** (#1234, closes #1228) by @pkupt
+  - New `SAPODataEntity` / `SAPODataConnector` / `SAPIngestor` (`semantica.ingest`, lazy exports), following the three-layer connector pattern already used for Snowflake/Databricks, to pull master/transactional data (Business Partners, Sales Orders) from SAP OData v2/v4 services into the Context Graph
+  - Dual auth (OAuth2 client-credentials for BTP/S4HANA Cloud, Basic for on-prem NetWeaver); every outbound request, including the token exchange, routes through `request_with_ssrf_guard`
+  - `$metadata` (CSDL XML) is parsed with a hand-rolled `xml.etree` reader rather than pulling in `pyodata`; pagination follows OData v2 `__next`/`__deferred` and v4 `@odata.nextLink`
+  - New `pip install semantica[ingest-sap]` extra (`requests>=2.28.0`)
+  - **Known phase-1 limits** (documented in docstrings): the OAuth2 token is cached but never refreshed, and pagination has no `max_pages` fuse (`top` bounds it when supplied)
+  - New `tests/ingest/test_sap_ingestor.py`: 22 tests (auth, EDMX parsing, v2/v4 pagination, SSRF routing, error paths, service-root normalization)
+
+- **`ContextGraph` gains deterministic, human-editable Markdown round-trip persistence** (#852) by @SaurabhScripts
+  - `save_to_markdown()`/`load_from_markdown()` write one file per node plus a graph manifest, so a graph can be reviewed and hand-edited outside the application without giving up the existing JSON API or its default behavior
+  - An existing destination is validated as a complete, canonical managed export before atomic replacement, so the loader can't silently clobber an unrelated or manually-extended directory
+  - Import/export paths and their ancestors reject symlinks, Windows junctions, and other reparse points, with pre-open and post-open validation — the same hardening applied to `AgentMemory`'s existing Markdown import in the companion fix below
+  - Dangling edge endpoints import as JSON-compatible entity stubs rather than being rejected outright (matching what the JSON loader already accepts); node/edge indexes, adjacency, and analytics/retraction/tombstone state are rebuilt after a Markdown load, and granular node/edge events are still emitted so temporal audit history stays useful
+  - New `tests/context/test_context_graph_markdown.py`: 29 passed, 1 skipped (the skipped case creates a real Windows junction and runs on Windows CI); full `tests/context/` suite: 614 passed, 1 skipped
+
+- **Explorer graph inspector gains a read-only Markdown content viewer** (#1078, closes #900) by @sakshi04-ui — Preview (rendered GFM) and Source (exact, whitespace-preserving) tabs for node content, with a copy-to-clipboard action. A URL allowlist restricts links to `http:`/`https:`/`mailto:`/in-document anchors, raw HTML execution is disabled, and external links carry `rel="noopener noreferrer"`. A first, focused step toward human-editable memory (#765); no write path yet. New `explorer/tests/markdownContentViewer.test.ts`: 8 tests
+  - **Follow-up (perf)** (#1195, addresses #1118) by @pravit-amp: `remarkPlugins` and the ~20-entry renderer `components` map were inline literals, so every unrelated re-render (e.g. clicking Copy) re-ran the full remark parse and remounted the whole subtree — up to 1.1s of main-thread block on a 2000-row GFM table. Both are now hoisted to module scope and the rendered element is memoized on content, cutting re-render cost from as much as 1121ms to ~0.1ms across all measured fixtures with no change to rendered output. A separate, upstream `remark-gfm` table-parse cost (~O(n^1.9), not fixed here) is left open on the issue as a product decision
+  - **Follow-up (cleanup)** (#1194, closes #1119) by @pravit-amp: the pure `isSafeUrl` URL-safety helper is extracted out of `MarkdownContentViewer.tsx` into its own `markdownUrlSafety.ts` module (behavior-preserving — moved verbatim), so the component module exports only components and stops tripping `react-refresh/only-export-components`
+
+- **`reasoning` gains a structured Action layer — rule-driven side effects with optional provenance** (#1096, closes #1095) by @cxzg007 — `AssertAction`/`RetractAction`/`CallAction`/`EmitEventAction` let a matched rule write facts back to a `KnowledgeGraph`, retract facts, call a structured handler (replacing the previously-unused `Rule.handler`), or emit to a sink registered via `Reasoner.on_event`, turning the reasoner from a pure inference engine into a production-rule system. With `provenance=True`, fired actions are recorded to `Reasoner.action_log`. Fully additive — rules without `actions` are unaffected, and the legacy `handler` field still fires (now wrapped internally as a `CallAction`). Also fixes a latent dangling import in `reasoning_provenance.py` (`ReasoningEngine`/`infer` → `Reasoner`/`infer_facts`). New `tests/reasoning/test_rule_actions.py`: 9 tests; full `tests/reasoning/` suite: 54 passed
+
+- **`run_shacl_validation` is now a public, documented entry point** (#1189, closes #1186) by @mikemikimike — the SHACL guide had documented the private `_run_pyshacl` helper as the canonical API; it's now exposed through `semantica.ontology`, with `_run_pyshacl` kept as a compatibility alias over the same implementation. `tests/ontology/test_ontology_advanced.py`: 33 passed (also fixes a flaky comparison against pySHACL's non-deterministic blank-node shape identifiers by comparing stable report fields instead)
+
+- **`docs/storage-backends.md`: adapter inventory and RDF/LPG feature matrix** (#899, addresses #888) by @yulinlina — which graph storage backends are built-in vs. bring-your-own, and where provenance/context support is partial
+- **`docs/guides/shacl-validation.md`: documented that `rdfs:range` + RDFS entailment makes `sh:class` unfalsifiable** (#1182, fixes #1130) by @ALDRIN121 — with entailment on, pyshacl infers the declared range class onto every object, so a `sh:class` constraint can never fail and reports `conforms: True` on non-conforming data; added to Common Pitfalls with the `inference="none"` vs `inference="rdfs"` contrast and guidance to re-run `sh:class` shape sets with entailment off before trusting a pass
+- **Cookbook: four new module notebooks** — `22_Provenance_Tracking.ipynb` (#989, lineage walks, revision history, invalidation, checksums), `23_Reasoning.ipynb` (#990, `Reasoner`/`DatalogReasoner`/`ExplanationGenerator`), `24_Change_Management.ipynb` (#991, versioned snapshots, named tags, checksum tamper-detection), and `25_Seed_Data.ipynb` (#992, bootstrapping a foundation graph from a trusted CSV source) — all by @LeonSGP43, filling gaps where the corresponding module shipped a usage doc but no runnable tutorial; every cell verified against current module source. `docs/cookbook.md` index entries for all four added in #1225
+- **README "Cite Us" section and `docs/citation.md` cross-link** (#1210) by @KaifAhmad1 — BibTeX/APA/MLA/Chicago/IEEE citation forms; also corrects the copyright holder in `LICENSE`/`docs/project-license.md` from the stale "Hawksight AI" to "Semantica" and replaces the retired `Hawksight-AI` GitHub org slug with `semantica-agi` across ~40 files (READMEs, issue templates, plugin manifests, cookbook notebooks, docs)
+
+### Changed
+
+- **A registered custom method can now refuse, instead of being silently overridden by the default implementation** (#1127, closes #1108) by @fabio-rovai — every module supporting custom methods wrapped the registered callable in a `try`/`except` that logged a warning and ran the built-in default on *any* exception, including one a validator or policy gate raised on purpose to say "do not produce this output." That made every registered gate advisory rather than authoritative. `semantica/utils/custom_methods.py` now centralizes the policy: an exception from a registered method propagates to the caller by default; `fallback_on_custom_error=True` restores the previous warn-and-continue behavior per call. Applied mechanically across all 58 call sites in `export/`, `ingest/`, `normalize/`, `parse/`, `embeddings/`, and `kg/` methods modules. New `tests/utils/test_custom_method_can_refuse.py`: 13 tests, including the reported gate-deletes-and-raises scenario and a guard that no call site still swallows
+- **Removed 13 confirmed-dead symbols across 9 files** (#1176, closes #1174) by @Vinv-AI — private helpers and Explorer app-layer code with zero callers in code, tests, or docs, none part of the public API or a FastAPI `response_model`; 289 deletions, no behavior change
+- **Consolidated the two duplicate Turtle/N-Triples literal escapers in `rdf_exporter.py`** (#1221, closes #1218) by @pkupt — `_escape_turtle_literal` (added in #1148) escaped the same five characters in the same order as the older module-level `_escape_literal`; the redundant one is dropped and all four call sites route through the original. Behavior no-op, verified against the full export suite (301 passed, 1 skipped)
+- **Removed the unreachable `_extract_with_spacy()` method and the unused `self.nlp` attribute from `NERExtractor`** (#1220, fixes #1058) by @yunaremaia — the ML dispatch path has always gone through `methods.py`'s process-level model cache instead; `__init__` still validates the spaCy runtime up front but no longer eagerly loads a model nothing on the instance reads
+- **Cleaned up an unused `sys` import and import ordering in `semantica/worker.py`** (#1061) by @aoright
+- **Test-only contributions**: isolated `sys.modules` mock leakage between `tests/visualization/` files so the suite passes in any collection order (#897, closes #859, by @luantaraschi); added coverage for 4 previously-untested `ConflictResolver` strategies and 3 `ConflictDetector` conflict types (#902, fixes #865, by @Devansh070); added a regression test tracking relationship provenance through `ProvenanceManager` (#1071, closes #1055, by @dex0shubham); added `max_tokens`-propagation regression coverage for LLM extraction methods, later folded into the cache-key fix below (#925, by @saiganesh47)
+
+### Fixed
+
+- **`SPARQLReasoner.execute_query()` claimed to run a query but always returned an empty result** (#1087, fixes #1083) by @ALDRIN121 — both the store-configured and unconfigured branches returned an empty `SPARQLQueryResult` with no real execution behind it, so a caller trusting "no matches" (e.g. a compliance check) could draw a false-negative conclusion from a method that never actually queried anything. Until a real triplet-store execution path lands, it now raises `NotImplementedError` explaining why, and the dead cache/inference scaffolding after the unreachable execution point is removed. 3 new regression tests
+- **`DuplicateDetector` merged entities that share no identifier, type, or name** (#1149, fixes #1137) by @pkupt — `_create_duplicate_candidate()` only ever boosted confidence for matching types and never penalized a mismatch, so two sparse, differently-typed entities (e.g. a `Person` and an `Organization`) could land above the merge threshold and collapse into one node, silently dropping the second. Two non-empty, differing types are now never a duplicate candidate. `tests/deduplication/`: 92 passed
+- **`TemporalGraphQuery.analyze_evolution()`'s `stability` metric was a hardcoded placeholder** (#1143, closes #1142) by @cxzg007 — every bounded relationship contributed a constant `1`, so `stability` was always `1.0` or `0` regardless of how long relationships actually stayed valid. Now computes the mean valid-time duration in seconds across relationships with both `valid_from`/`valid_until` set; unbounded/half-open intervals are skipped and negative intervals clamp to zero. 3 new tests in `tests/kg/test_kg.py`
+- **CodeQL false-positive on a JSON-LD test's URL check** (#1183) by @KaifAhmad1 — `"https://schema.org/" in flattened` pattern-matched CodeQL's substring-sanitization heuristic even though `flattened` is always a `list` (exact membership, no sanitization or SSRF path involved); rewritten as an explicit `any(entry == ... for entry in flattened)` with identical behavior
+- **HuggingFace NER extraction crashed on `huggingface_model` being forwarded as an unexpected pipeline loader kwarg** (#1188, fixes #1063) by @shahzaib-ahmadcs — while preserving genuinely supported pipeline kwargs like `aggregation_strategy`. 5 tests pass
+- **JSON-LD document/graph `@id` was minted from the wall clock, so re-exporting an unchanged graph produced a new subject every time** (#1181, closes #1147) by @reddynitish — merging repeated exports duplicated graph identity instead of recognizing them as the same graph. The `@id` is now content-derived, with optional `graph_uri`/`document_uri` overrides for callers with a stable graph name; `semantica:exportedAt` still records export time separately. Applies to both JSON-LD export paths
+- **`ContextGraph.get_causal_chain()` only matched the canonical uppercase causal-edge spellings, silently missing edges recorded in `CausalChainAnalyzer`'s present-tense vocabulary** (#1187, fixes #1184) by @ALDRIN121 — `causes`/`influences`/`precedes` differ from `CAUSED`/`INFLUENCED`/`PRECEDENT_FOR` in word form, not just case, so an edge recorded with the analyzer's spelling produced an empty audit chain — silent, and in the dangerous direction for a compliance trace. `add_causal_relationship()` now normalizes through an alias map before storing the canonical form; traversal accepts the union vocabulary. 2 new regression tests, full `tests/context/` suite: 587 passed
+- **`semantica embed generate` corrupted its own output and could recurse into a stack overflow** (#996/#1004/#1005, closes #994) by @varunsahni18, @yzxcj797 — three compounding defects in one pipeline. (1) `generate_embeddings`/`embed_text`/`calculate_similarity`/`pool_embeddings` all registered themselves as their own custom-method-registry default, so an unqualified call (exactly what the CLI does) re-entered the same wrapper until Python's recursion limit; each of the four dispatch sites now guards on registry identity before recursing (#996, #1005). A second self-recursion in `EmbeddingGeneratorWithProvenance.__getattr__` (re-entering itself when `_generator` is unset, e.g. during a `deepcopy` probe) now raises a normal `AttributeError` for private names instead (#1005). (2) `--output embeddings.parquet` wrote `json.dumps(result, default=str)` regardless of extension, turning a numpy array into its plain-text `repr()` — a file `embed index` then failed to open as Parquet; the writer now detects `.parquet`/`.json`/`.jsonl` and produces real Parquet/JSON, rejecting any other extension with a clear message (#996, #1004). (3) `pyarrow` was only in optional extras despite being required by the documented quick-start flow; promoted to a core dependency (#996)
+- **`AgentMemory`'s existing Markdown import accepted symbolic links, NTFS junctions, and other Windows reparse points** (#851) by @SaurabhScripts — a direct linked import path is now rejected with an actionable error, and a linked entry found inside an otherwise-valid directory is skipped rather than aborting the whole import; hardened with pre-open/post-open checks, `O_NOFOLLOW` where available, and `fstat`-based regular-file validation. `tests/context/`: 595 passed, 1 skipped (Windows-junction test, runs on Windows CI)
+- **A caught vector-similarity scoring exception left stale partial state behind, risking a misleading match on the next call** (#885, fixes #875) by @ArmanGrewal007 — the exception is now logged at debug level and `vector_score`/`vector_idx` reset to neutral values before the remaining matching stages continue
+- **`RDFExporter` could write invalid or unintended relative IRIs for `GraphBuilder`-default entity/relationship identifiers** (#1112, closes #1099) by @mikemikimike — normalization is now applied at the RDF export boundary across Turtle (including temporal Turtle), RDF/XML, and N-Triples: bare/relative identifiers are minted under the Semantica namespace with safe percent-encoding, absolute IRIs pass through unchanged, and configured/input-context prefixes expand through the effective namespace mapping. 38 focused regression tests; 175 export tests plus 46 subtests pass
+- **`RDF4JStore`'s `repository_id` constructor argument had no effect** (#1192, closes #1191) by @Freakz2z — the explicit id is now honored when selecting the repository; stale documentation caveats claiming otherwise are removed. 65 tests pass across the affected triplet-store suites
+- **Non-interactive stdout (piped/redirected output, CI logs) was flooded with progress-bar escape sequences** (#1193, fixes #1185) by @ALDRIN121 — a plain `python demo.py > out.txt` captured 173 bytes of progress noise around 10 bytes of real output. `ProgressTracker` now attaches its console display only for an interactive terminal, Jupyter, or the new `SEMANTICA_FORCE_PROGRESS` opt-in (following the `NO_COLOR`/`FORCE_COLOR` convention); file-based progress logging is untouched. Both switches are now documented in the README and `docs/reference/utils.md`. 11 tests pass (6 new)
+- **Entity `metadata` was dropped by every RDF serializer except the JSON-LD path**, so an entity kept its confidence but lost its source document, page, extractor, and reviewer on Turtle/N-Triples/RDF/XML/`RDFExporter`'s own JSON-LD (#1165, closes #1154) by @fabio-rovai — Semantica's own metadata keys (`num_entities`, `snapshot_time`, Neo4j loader fields, etc.) are now mapped to declared vocabulary terms and carried through on every path; a caller-supplied key with no mapped term is skipped with an explicit warning (rather than silently vanishing) naming the override needed, pending the caller-key namespace decision tracked in #1146. 21 new tests in `tests/export/test_metadata_passthrough.py`; `tests/export`+`tests/ontology`: 274 pass
+- **`extract_relations_llm` silently dropped caller-supplied generation parameters** (`max_tokens`, `top_p`, `seed`, etc.), and the extraction cache didn't distinguish calls made with different generation settings (#1213, with test coverage from #925) by @Sameer6305 — a small hardcoded allowlist forwarded only `temperature`/`verbose` to `generate_typed`, discarding the rest; fixed by forwarding all caller kwargs. Once forwarded, those parameters also needed to enter the cache key, since two calls differing only in `max_tokens` previously shared one cache entry and the second could silently reuse a result generated under the first's settings — now applied consistently across entity, relation, and triplet LLM extraction. New regression tests for cache bypass/reuse under differing `max_tokens`/`temperature`
+- **`OxigraphStore` silently ignored the `storage_path` constructor argument and never flushed writes before a reopen**, both causing silent on-disk data loss (#970) by @logan-jl-cc — `__init__`'s parameter is named `path`, so the project-conventional `storage_path` landed in `**config` and was ignored, degrading a supposedly-persistent store to in-memory with no error; `storage_path` is now accepted as an alias. Separately, pyoxigraph's background flush can lag behind a write, so a reopen immediately after `add_triplets` could observe fewer triples than were written; writes to an on-disk store now call `flush()` explicitly. 2 new regression tests, full suite: 9 passed
+- **MCP server's `export_graph` tool was broken on every output format** (#1151) by @Arasz — the `json` branch called `JSONExporter().export()` without the `file_path` it requires, and every RDF branch passed a `ContextGraph` object where the exporters expect the canonical kg dict, both surfacing as a raw exception string. A third bug compounded both: the RDF export path's progress bar wrote to stdout, which over stdio MCP *is* the JSON-RPC framing, corrupting the protocol and hanging the client (a 300s timeout on an empty graph). Fixed by converting through `ContextGraph.to_kg_dict()`, serializing the JSON branch to match the RDF branches' string contract, and forcing `SEMANTICA_DISABLE_PROGRESS=1` for the server process. 5 new tests, verified failing against 0.6.6 beforehand
+- **`OntologyIngestor` dropped every class and property from a JSON-LD document using a named graph** (#1156, fixes #1129) by @13g4d0 — a top-level `@id` beside `@graph` names the graph, and `rdflib.Graph.parse()` silently loads only the default graph, discarding the rest; `POST /api/ontology/load` returned `status: "success"` with `class_count: 0`. Now parses into a `Dataset` and flattens all quads into the working graph (the same `Graph`→`Dataset` migration #757 made for `JenaStore`, extended to the ingest path). On the PR's real-world reproduction: 25 triples/1 subject before, 719 triples/45 classes/40 object properties after. 4 new tests including a default-graph canary so the fix can't trade one blind spot for another
+- **Turtle and N-Triples RDF export interpolated entity `text` into string literals with no escaping**, so a `"`, backslash, newline, CR, or tab in the source text emitted invalid RDF other parsers rejected (#1148, closes #1098) by @pkupt — a shared `_escape_turtle_literal()` (later consolidated in #1221) now escapes per the RDF 1.1 Turtle grammar and is reused for the N-Triples path, which previously escaped only quotes and newlines. `tests/export/`: 161 passed, 1 skipped
+- **`PipelineSerializer` round trips dropped step dependencies and delta-processing metadata, and could rehydrate a legacy stringified handler as a non-callable string** (#1217, fixes #1216) by @cxzg007 — step dependencies, delta mode, and base/target version IDs are now restored from the serialized schema; runtime handler callables are treated as process-local state and excluded from serialized business configuration rather than (mis)serialized. 52 tests pass
+- **`PipelineBuilder` never actually dispatched to a handler registered by `step_type`**, and a serialize/deserialize round trip could leak `handler`/`dependencies` into a step's business config (#1215, fixes #1214) by @cxzg007 — a registered handler is now resolved by `step_type` when no explicit `handler=` is supplied (explicit handlers still take precedence), and the two builder-control fields are kept out of `PipelineStep.config` so a strict handler signature can't receive them as unexpected kwargs. `tests/core`+`tests/pipeline`: 50 passed
+- **`PipelineBuilder.set_parallelism()` was accepted and stored but never read — pipeline steps always ran strictly sequentially**, and the setting didn't survive a serialize/deserialize round trip (#1226, fixes #1223) by @cxzg007 — wired through builder → serializer → execution engine, plus a new opt-in `PipelineStep.parallel_safe` flag. A dependency layer now runs in parallel only when every step in it is marked `parallel_safe`, the layer has more than one step, the input is dict-typed, and no step is in delta mode; otherwise it falls back to sequential execution. Each parallel step's input is deep-copied for isolation, execution is bounded by `ThreadPoolExecutor(max_workers=min(configured parallelism, max_workers))`, a failure cancels pending futures in the layer, and layer results merge back in declaration order (a same-key conflict raises `ProcessingError`). 22 new tests in `tests/pipeline/test_pipeline_parallel.py`
+- **`Config.get()` silently dropped boolean environment-variable overrides** (#1038, fixes #1035) by @Kyou12138 — the type dispatch checked `isinstance(default, int)` before `isinstance(default, bool)`, and since `bool` subclasses `int` in Python, the bool branch was unreachable: `CONFLICT_ZZTESTFLAG=true` with a `False` default returned `False`, and `=1` returned the int `1` rather than `True`. Bool is now checked first (with whitespace stripped before parsing truthy/falsy spellings), fixed across all ten affected config modules (`conflicts`, `deduplication`, `split`, `embeddings`, `export`, `ingest`, `kg`, `parse`, `ontology`, `normalize`). 12 new tests plus 6 existing conflicts tests and 131 related module tests pass
+- **Scanned (image-only) PDFs parsed with no error and no warning, returning empty text with a "completed" status** (#1021, closes #1020) by @shanyu910 — `PDFParser._parse_page` swallowed a missing text layer via `page.extract_text() or ""`, so the failure only surfaced far downstream as zero extracted entities. A warning now fires when every parsed page yields no text with `extract_text` enabled, pointing at `parse_pdf(..., method="docling", enable_ocr=True)`. Also fixes a separate `import semantica.parse` failure on a fresh interpreter (`email_parser.py` used `email.message.Message` without importing `email.message`) that was blocking the parse test suite from even collecting. 25 tests pass in `tests/parse/`
+- **`GET /api/decisions` returned HTTP 422 for any graph containing real decisions**, breaking the Explorer Decisions workspace entirely (#937) by @logan-jl-cc — `record_decision()` stores the timestamp as a POSIX float, but `DecisionResponse.timestamp` is typed `Optional[str]` and Pydantic's strict mode rejected the coercion. Fixed by coercing to `str` (preserving `None`) at the response-adapter boundary
+- **Decision persistence/query bugs, CJK text handling, and three missing MCP graph tools** (#967) by @toratto — `mcp_server`'s `_get_graph` called a non-existent `graph.load` instead of `load_from_file`, so `SEMANTICA_KG_PATH` was silently ignored and the server always started with an empty graph; `query_decisions` read `category` from the wrong field, always returning nothing for a category filter; `find_precedents`/`query_decisions(query=)`'s similarity threshold was too high for short CJK queries, which also failed outright because `_calculate_decision_content_similarity`'s whitespace-Jaccard fallback is always zero for languages with no whitespace tokenization (now falls back further to a character-bigram overlap coefficient); `load_from_file` didn't rebuild the in-memory decision/entity/temporal indexes after loading, breaking `find_precedents_by_scenario` and decision counts post-reload; `extract_entities`/`extract_relations` returned the spaCy type label as `text` and dropped the actual entity text, and had no way to select a non-English NER model. Also adds three new MCP tools (`query_graph`, `update_node`, `delete_node`, the latter two persisting back to `SEMANTICA_KG_PATH`)
+- **`sqlalchemy.text` was used but never imported in two `DBIngestor`/`DataExporter` methods**, raising `NameError` on every call before any query reached the database (#1017, closes #1015) by @pravit-amp — `connect()`/`test_connection()` imported `text` function-locally, so the binding never reached `export_table_data()` or `execute_query()`, which called it anyway; both raised immediately, re-wrapped by an `except Exception` into a `ProcessingError` that read like a database fault rather than a missing import. `docs/guides/ontology.md` documents `DBIngestor().execute_query()` as a supported entry point, so documented usage walked straight into it. 5 new tests against a temporary SQLite database, also repairing a previously-failing `tests/ingest/test_notebook_02.py` case
+- **Ontology generation resolved relationship endpoint types incorrectly, producing wrong object-property domains/ranges** (#1170, closes #1168) by @T1mn — endpoint types are now resolved from the canonical `source_id`/`target_id` fields and supported aliases instead of defaulting to the first entity when a field was missing, preventing e.g. a `Person -> Organization` relationship from generating a `Person -> Person` property. 80 tests pass, 1 skipped
+- **Ontology property generation dropped data properties when a raw entity type was normalized into a class name** (#1171, closes #1169) by @T1mn — e.g. `software engineer` → `SoftwareEngineer` lost its `email` property; attributes are now grouped by matching raw, normalized, and recorded class names, so the normalized class stays each property's domain. 79 tests pass, 1 skipped
+- **`flatten_dict()` silently dropped data when a top-level key already containing the separator collided with a key produced by flattening a nested dict** (#1012, fixes #1010) by @yzxcj797 — `{"a.b": 1, "a": {"b": 2}}` flattened to `{"a.b": 2}` with no error, the `1` simply gone; collisions are now detected (unique-key count vs. item count) and raise `ValueError` naming the colliding key before data is lost. 6 new tests
+- **Creating relationships after `GraphStore.add_edges`/`build_from_entities_and_relationships` silently produced zero edges against ID-minting backends** (#1173, fixes #1136) by @yzxcj797 — an id-space mismatch across three layers: `add_edges` reads application-level string ids and passes them to `create_relationship`, which is a pure passthrough into `Neo4jStore.create_relationship`'s `MATCH ... WHERE id(a) = $start_id` — a Neo4j-internal integer id. Every node was created and every relationship silently failed with one easily-missed warning per edge. `GraphStore` now keeps an application-id→internal-id map, populated by `add_nodes`/`create_node` from the backend's own creation results and consulted by `create_relationship`; unknown ids and identity-mapped backends are unaffected. `tests/graph_store/`: 100 passed
+- **RDF export left `semantica:text`/`rdfs:label` empty for entities that only carry a `name` field**, across all four RDF formats (#1113, fixes #1097) by @cxzg007 — `RDFSerializer.convert_kg_to_rdf()` already implemented the `name`→`label`/`text` normalization, but `export_to_rdf()` never called it. Now called once at the export boundary (idempotent, non-destructive, falls back to a label derived from the id suffix). 7 new tests, `tests/export/test_rdf_exporter.py`: 17 passed
+- **Docker Explorer image failed to build on Python 3.14** — `gensim` has no prebuilt wheel for it and the slim base has no `gcc` to build from source (#1172, closes #1025) by @DwitiThaker — runtime pinned to `python:3.13-slim`, where `gensim` installs from a prebuilt wheel
+- **Unit normalization rejected common aliases before conversion** — `kg`, `g`, and other abbreviated/plural unit spellings failed category validation and the conversion-factor lookup ahead of it (#939) by @Mr-Neutr0n — aliases now normalize first; canonical aliases added for feet, yards, miles, and gallons. 7 tests pass
+- **An oversized, caller-controlled mapping key could blow up a `ValidationError` message to megabyte scale**, and equally inflate application logs on repeated malformed input (#1088, fixes #1001) by @ALDRIN121 — follow-up to the graph-payload validation added in #958. The displayed key is now truncated at 64 characters with an ellipsis; the underlying input and validation decisions are unchanged. 4 new tests
+- **`SeedDataManager.load_from_api()` mislabeled genuine connection failures as a missing `requests` dependency** (#972, closes #949) by @pravit-amp — `requests.exceptions.RequestException` (connection errors, timeouts, `raise_for_status()` failures) subclasses `OSError`, so an `except (ImportError, OSError)` block written to guard a lazy import that no longer existed (`requests` is a core dependency) caught real failures too and told users to reinstall an already-installed library while dropping the original exception chain. The block is removed; genuine failures now surface through the existing `Failed to load from API: {e}` path with `from e` intact. 5 new regression tests
+- **`SHACLGenerator` produced shapes that matched nothing, and pySHACL reported `conforms: True` on data that plainly violated them** (#1124, closes #1104, closes #1105) by @fabio-rovai — `base_uri` was used both as where shape resources live and to expand every `sh:targetClass`/`sh:path`, so with the default shapes namespace, generated shapes targeted classes no data graph in the package actually uses; a shape with zero matching focus nodes is vacuously satisfied, so validation silently passed regardless of real violations. The target namespace now resolves independently (explicit argument → ontology's declared namespace → an existing absolute class/property IRI → ontology `uri` → the vocabulary namespace), never the shapes namespace. Separately, `_attach_property_shapes` attached a domain-less property's constraint to *every* shape ("no domain declared, attach to all"), asserting a constraint the ontology never stated; a domain-less property is now left unattached by default, with `attach_domainless_properties=True` to restore the old behavior. 17 new tests validate real data through pySHACL rather than reading shape text; `tests/ontology`+`tests/export`: 239 passed
+- **OWL export dropped every generated property and collapsed distinct classes onto one node** (#1123, closes #1103) by @fabio-rovai — `OWLExporter` reads `object_properties`/`data_properties`, but `OntologyGenerator` emits one combined `properties` list, so every property was silently discarded; separately, a class built without a namespace manager gets `"uri": None`, which a `"uri" not in cls"` guard never catches (the key is present), so the exporter wrote a relative `<>` IRI for it — resolved by rdflib against the current working directory, meaning two classes could collapse onto one subject and that subject's identity changed with the export's working directory. Both dict shapes are now merged and classified correctly, and a class/property IRI resolves through `uri`→`iri`→`id`→a name joined onto the ontology base, skipping (with a warning) a term with none of those instead of minting `<>`. 10 new regression tests parse the real output with rdflib and Oxigraph; `tests/export`+`tests/ontology`: 231 passed
+- **Confidence scores serialized as four different, mutually-disagreeing RDF terms depending on export format, and one non-numeric confidence value could break an entire Turtle export** (#1125, closes #1100, closes #1102) by @fabio-rovai — Turtle wrote a bare `xsd:decimal`, N-Triples an explicit `xsd:float`, RDF/XML an untyped plain literal, and JSON-LD's native number expanded to `xsd:double`; loading a Turtle and an N-Triples export of the same graph into one store gave the same entity two different confidence values. Separately, an unparseable confidence (e.g. the string `"high"`) was interpolated into Turtle with no validation, producing a syntax error that dropped every entity from the export. All four paths now write one canonical `xsd:decimal` lexical form (matching the pre-existing Turtle behavior and the only exact representation of the four); an unusable value is omitted with a warning instead of corrupting the document. The vocabulary's `sem:confidence` now declares `xsd:decimal` (previously left undeclared to avoid contradicting the disagreeing exporters). 20 new tests compare parsed graphs across all four formats; `tests/export`+`tests/ontology`: 240 passed
+- **An OWL-Time validity interval was reified onto a relationship IRI the graph never actually referenced**, making it unreachable from the edge it described (#1126, closes #1106) by @fabio-rovai — a relationship serializes as a single triple with no node of its own, so `include_temporal=True` minted a well-formed `time:Interval` with zero inbound arcs to its subject. Turtle now also emits the `sem:Relationship`/`sem:source`/`sem:target`/`sem:type` reification the JSON-LD path already produced, but only when there's temporal data to attach — default and `include_temporal=False` output are byte-for-byte unchanged. 7 new tests include a SPARQL walk from the edge to its interval, the path the dangling node made impossible; `tests/export`+`tests/ontology`: 228 passed
+- **JSON-LD exports were unreadable by Semantica's own default parser** (#1145, fixes #1144) by @fabio-rovai — every export was written as a named graph (a top-level `@id` beside `@graph`), which a plain `rdflib.Graph.parse()` silently discards in favor of the (empty) default graph; a two-entity graph parsed as 2 triples instead of 20. Compounded by `export_knowledge_graph` converting its payload to JSON-LD and then handing the *already-converted* document to `export()`, which converted it again, producing two `@context` blocks and two document nodes. Metadata now attaches beside `@graph` rather than naming it, and a payload that already declares `@context` is merged rather than re-wrapped. 9 new tests parse with both `Graph()` and `Dataset()` and assert identical counts; full-suite failure set unchanged before/after (539/539)
+- **`GraphBuilder` didn't propagate entity-resolution's merged ids into the `source_id`/`target_id` relationship aliases**, only `source`/`target` (#1115, closes #1110) by @T1mn — a relationship's alias fields could still point at a pre-merge id after resolution. Both alias pairs are now kept in sync. 9 tests pass
+- **`GraphValidator` indexed entities only by `id`, rejecting graphs that use the `entity_id` alias as invalid even when their relationships were fine** (#1116, closes #1111) by @T1mn — validation and endpoint checks now go through the shared `get_entity_id()` helper, accepting both fields consistently. 5 tests pass
+- **Broken star history chart in README** (#1057) by @OctoBored — the embedded chart used the GitHub stargazer API, now access-restricted; switched to a token-free alternative data source
+
+### Security
+
+- **Agno's `AgnoKnowledgeGraph.load_urls()` made outbound requests with no SSRF protection beyond a scheme check** (#1212) by @Sameer6305 — caller-supplied URLs went straight to `urllib.request.urlopen()`, unguarded against loopback/private addresses, cloud metadata endpoints (`169.254.169.254`), IPv6-internal addresses, hostnames resolving to private space, or redirects into any of the above. Found during a project-wide SSRF audit following #936/#959. Now routed through the shared `request_with_ssrf_guard()`; an unsafe URL is skipped rather than aborting the rest of the ingestion batch. `OpenClawKGTool` (operator-configured, intentionally allowed to target `localhost` for local deployments) gains scheme/malformed-URL validation as defense in depth, without restricting its legitimate private-network use case. 29 new Agno tests, 26 new OpenClaw tests, all passing alongside the 15 pre-existing Agno integration tests
+
+### Dependencies
+
+- Routine version bumps with no application-facing behavior change: `anthropic` 0.121.0→0.122.0 (#1045), `botocore` 1.43.69→1.43.73 (#1047), `agno` 2.8.7→2.9.0 (#1050), `google-genai` 2.17.0→2.18.1→2.19.0 (#1163, #1205), `lxml` 6.1.1→6.1.2 (#1197), `charset-normalizer` 3.5.0→3.5.1 (#1201), `pypickle` 2.0.1→2.0.2 (#1203)
+
+## [0.6.6] - 2026-08-20
+
+### Added
+
+- **Semantica RDF vocabulary, and deterministic entity/relationship IRIs** (#1109, closes #1107, closes #1101) by @fabio-rovai, reviewed by @KaifAhmad1
+  - Every RDF/JSON-LD export mints terms in `https://semantica.dev/ns#`, and until now nothing declared what those terms meant — the namespace 404s and no vocabulary shipped with the package, so a consumer receiving an export had no way to tell `sem:text` from a typo of it, and no closed-world checker could validate an export at all
+  - `semantica/ontology/vocabulary/semantica-ns.ttl` declares the terms the exporters actually emit — drawn from the emitting call sites in `export/rdf_exporter.py`, `export/json_exporter.py` and `provenance/manager.py`, not from what a vocabulary "ought" to contain. Ships inside the package (`from semantica.ontology.vocabulary import vocabulary_turtle`) so it loads without a network round trip, and is the same document intended to be served at the namespace IRI once hosting/content-negotiation is sorted
+  - `tests/ontology/test_vocabulary.py` ties the document to the code: every term a serializer can write must be declared, so adding a term to an exporter without declaring it fails the build
+  - The missing-id fallback minted entity/relationship IRIs from Python's builtin `hash()`, randomised per process (`PYTHONHASHSEED`), so the same entity got a different IRI on every run and exports couldn't be diffed, deduplicated, or joined to an earlier provenance record. It also wrote `<semantica:entity_N>`, an IRI in the scheme `semantica` rather than the expansion of the declared prefix, so those nodes never joined with anything written through it. Minting now uses SHA-256 and writes a full IRI in the declared namespace; the same fix applies to the default entity/relationship types in the Turtle path
+  - **Fixed during review** (Qodo): the temporal fallback minted from `source_id` only, while the main serializer accepts `source_id` or `source` — relationships using the second form hashed two empty strings, which the previous randomised `hash()` masked by making the IRI unstable anyway; once deterministic, unrelated relationships at the same list index collided on one IRI across exports. Endpoints are now resolved the same way `serialize_to_turtle` resolves them, before minting. `sem:confidence` also lost its declared `xsd:decimal` range: the N-Triples serializer types the same value `xsd:float`, and the two are disjoint, so declaring either contradicted one of the exporters (tracked in #1100) — a new `test_declared_ranges_do_not_contradict_what_the_exporters_emit` guards the whole class of that mistake
+  - **Fixed in follow-up**: `serialize_to_rdfxml`'s default entity type still wrote the bare string `"semantica:Entity"` into an `rdf:resource` attribute, which (unlike a Turtle angle-bracket or an XML element name) is not namespace-expanded — the exact #1101 failure mode, just on the untested RDF/XML path. `json_exporter.py`'s `semantica:format` and `@type: "semantica:KnowledgeGraph"` were emitted but absent from both the vocabulary and the test's `EMITTED_TERMS` guard set, so the "undeclared terms fail the build" claim didn't actually cover them — both are now declared and guarded. `MANIFEST.in` didn't mirror the `pyproject.toml` package-data addition, so a source-distribution install could omit the vocabulary file. The cross-process minting-stability test replaced the subprocess's entire environment with a POSIX-only `PATH`, breaking it on Windows; now overrides only `PYTHONHASHSEED` on top of the inherited environment
+  - **Also fixed, on the JSON-LD paths**: the first fix covered the Turtle, N-Triples and RDF/XML serializers, and left both JSON-LD writers interpolating the entity's own text into `f"semantica:entity/{text}"` and the endpoints into `f"semantica:rel/{source}_{target}"`. Three consequences, all live in 0.6.5: an entity whose text contained a space produced an invalid IRI, and a JSON-LD parser dropped that node in full rather than reporting it, so the entity disappeared from the export; every relationship carrying `source`/`target` rather than `source_id`/`target_id` minted the identical `semantica:rel/_`, collapsing all of them onto one node whose types and endpoints merged; and the JSON-LD `@id` disagreed with the Turtle IRI for the same entity, so the two serializations of one knowledge graph were two different graphs. Both JSON-LD writers now use `mint_entity_iri`/`mint_relationship_iri`, and `JSONExporter.export_entities`/`export_relationships` declare the `semantica` prefix their `@context` was already writing `semantica:entities` against — without it a processor reads that as an IRI in the scheme `semantica`, which is the original #1101 defect on a third path
+  - `tests/export/test_jsonld_iri_minting.py` parses each export with a real JSON-LD processor and asserts the entity survives, the relationships stay distinct, no term expands into the `semantica` scheme, and the JSON-LD `@id` equals the Turtle IRI
+  - 236 export and ontology tests pass
+
+- **First-class CrewAI integration** (#988, closes #962) by @Shindevrp
+  - New `pip install semantica[crewai]` extra (`crewai>=0.80.0`) — crewai core provides `BaseTool`/`BaseKnowledgeSource`, so `crewai-tools` is intentionally not included, and the extra is intentionally **not** part of the `all` bundle: crewai hard-requires `chromadb~=1.1.0`, which is affected by the unpatched pre-auth code-injection CVE-2026-45829 (see `integrations/crewai/README.md`)
+  - `integrations/crewai/SemanticaKGTool` — a CrewAI `BaseTool` exposing 5 KG actions (`extract_entities`, `extract_relations`, `add_to_graph`, `query_graph`, `find_related`) backed by `NERExtractor` / `RelationExtractor` / `ContextGraph`; supports both sync `run()` and async `arun()`
+  - `integrations/crewai/SemanticaDecisionTool` — a CrewAI `BaseTool` wrapping `AgentContext` with 5 decision-intelligence actions (`record_decision`, `find_precedents`, `trace_causal_chain`, `analyze_impact`, `check_policy`)
+  - `integrations/crewai/SemanticaKnowledgeSource` — a CrewAI `BaseKnowledgeSource` that serializes a `ContextGraph` into crew knowledge storage; implements both the legacy `load_content()` and current `validate_content()`/`aadd()` contracts so it works across `crewai>=0.80.0`
+  - All three classes degrade gracefully when `crewai` is not installed (still importable, full Semantica API available)
+  - New `tests/integrations/crewai/`: 70 tests covering stub-based present-case behavior (Pydantic/BaseTool subclassing, every action, knowledge-source chunking/storage) plus a subprocess isolation test for the crewai-absent degradation path
+  - Docs: `docs/integrations/crewai.md` page, `docs.json` Integrations nav entry, and README integration-matrix/install updates
+  - **Hardened during code review**: live `graph`/`context`/extractor state is excluded from CrewAI JSON serialization (`model_dump(mode="json")`) with `model_post_init` self-healing defaults, so checkpoint/resume no longer raises `PydanticSerializationError`; `query_graph` now searches node content (not just ids/types); `trace_causal_chain` returns an explicit error instead of substituting similarity precedents when causal tracing is unavailable, and calls `trace_decision_causality(..., max_depth=...)` with the correct argument name; `find_precedents` propagates `max_precedents` as the backend `limit`; `add_to_graph` writes are serialized under a module lock so concurrent agents can't double-count duplicate adds; nameless entities are skipped instead of creating `repr()`-junk nodes
+  - **Hardened during second code review**: `check_policy` rules are now coerced type-aware — `bool("false")` was truthy, so `enabled == false` reported a violation for `enabled: false`, and string datums like `"0.90"` were compared lexicographically instead of numerically; `trace_causal_chain` no longer raises `AttributeError` (which escaped the tool) when the decision context has no `knowledge_graph`, returning honest error JSON instead; knowledge-source storage failures log an actionable ERROR (a missing crew embedder otherwise silently left agents with empty retrieval); `add_to_graph` uses a per-graph re-entrant lock instead of a process-global one (independent graphs no longer serialize each other, and re-entrant extractors can't deadlock); entity/relation `confidence=None` normalizes to `1.0` instead of failing the whole extraction; added a subprocess integration test against the real `crewai` package covering `Crew`-level serialization round-trip and restore
+
+- **`ContextGraph` gains retraction and purge — the graph previously had no way to remove a node or edge without discarding everything via `clear()`** (#957, closes #955) by @pravit-amp, reviewed by @KaifAhmad1
+  - `retract_node()`/`retract_edge()` close an entity's validity window rather than deleting it, reusing the existing `valid_from`/`valid_until`/`state_at()` machinery: the entity drops out of `find_active_nodes()` and future `state_at()` queries going forward, but `state_at()` calls before the retraction time still return it, so decisions recorded against it stay explainable. A `("kind", id)`-keyed retraction record captures who/why/when, retrievable via `get_retraction()`/`list_retractions()`
+  - `purge_node()`/`purge_edge()` are the destructive counterpart: the entity is removed outright, from history as well as the active view, for erasure obligations retraction alone cannot satisfy (e.g. GDPR Article 17). Only a tombstone remains — that a purge happened, when, and why — deliberately never the purged content, via `get_tombstone()`/`list_tombstones()`. Purge is graph-scope only: `AgentMemory` and any bound vector store are not reached, so it is one step of an erasure workflow rather than the whole of it
+  - Both operations default to `cascade=True` (also touching every incident edge, and for `purge_node`, the marker node of any cross-graph link the node exits through) since leaving edges active around an inactive/removed node produces an inconsistent active view or dangling endpoints; both accept `cascade=False` for callers that want to handle edges themselves
+  - Both are idempotent: retracting/purging an already-retracted/purged entity returns `False` rather than raising, and a repeat retraction preserves the original record's reason rather than overwriting it
+  - Retraction/purge closing a validity window never widens an existing one — a node or edge added with `valid_until` already in the past keeps that earlier bound rather than being pushed later by a subsequent retraction time
+  - Reuses the existing audit-trail path with no changes to `change_management`: `MutationRecord` already documented `REMOVE_NODE`/`REMOVE_EDGE` in its operation vocabulary; retraction now emits `UPDATE_NODE`/`UPDATE_EDGE`, purge emits `REMOVE_NODE`/`REMOVE_EDGE`, matching the documented contract. Mutation payloads are snapshotted inside the lock and the callback fires after it is released, so a callback that itself mutates the graph (e.g. `clear()`) can't observe or lose in-flight records
+  - **Fixed during review** (@KaifAhmad1): `retract_edge()`/`purge_edge()` resolved "the edge" for a given `edge_id` via the first matching object only. `edge_id` is content-derived and, prior to #926, was not guaranteed unique — a graph holding two identical `add_edge()` calls had two edge objects sharing one id. A direct `retract_edge()`/`purge_edge()` call would silently leave the second duplicate untouched (still live, still active) while returning `True` and recording a tombstone/retraction that claimed the edge was fully handled; repeat `purge_edge()` calls also silently overwrote the tombstone's `reason`/`purged_at` on each partial attempt instead of no-op'ing. The same gap let `retract_node()`'s cascade skip a duplicate outright, since it checked the live `_retractions` dict mid-loop and treated the first duplicate's just-written record as proof the second was already handled. `#926` (merged) stops *new* duplicates from being created, but any graph already holding one — loaded from a save made before that fix, or built during the window before it landed — could still trigger this. Now `retract_edge()`/`purge_edge()` act on every edge matching the id under one record, and the cascade's dedup check is snapshotted before the loop starts so within-call duplicates are still closed rather than skipped. 5 new regression tests in `TestDuplicateEdgeId`
+  - New `tests/context/test_context_graph_retraction.py`: 49 tests, covering retraction/purge semantics, cascade, idempotency, validity-window narrowing, id-keyspace collisions between node and edge ids, cross-graph link teardown, `clear()`/`load_from_file()` resetting retraction/tombstone state, audit-trail integration against a real `TemporalVersionManager`, mutation-emission ordering under a concurrent `clear()`, and concurrent purges
+  - Full `tests/context/` suite: 533 passed
+- **`DistanceExporter.compute_pairs()` gains an opt-in `metric_errors` column to distinguish legitimate `None` results from computation failures** (#960, follow-up to #879) by @Karunasagar12
+  - Previously, a `None` in `hop_count`/`weighted_distance`/`semantic_similarity`/betweenness could mean either "no path exists" or "the underlying computation raised" — logged as a warning per #879, but not otherwise surfaced, so the two cases were indistinguishable in exported CSV/JSONL/DataFrame data. `include=["metric_errors"]` now adds a `metric_errors` field per row: `""` when all requested metrics succeeded, or a comma-separated list of metric names that raised (e.g. `"hop_count,weighted_distance"`)
+  - Opt-in only — default `compute_pairs()`/`to_csv()`/`to_dataframe()`/`to_jsonl()` schema is unchanged unless `"metric_errors"` is explicitly requested
+  - The four metric helpers (`_betweenness`, `_hop_distance`, `_weighted_distance`, `_semantic_similarity`) now return `(value, error_name | None)` tuples internally; `compute_pairs()` aggregates the error names per row
+  - **Fixed during review** (Qodo): `_betweenness()` failures weren't tracked into `metric_errors` in the initial version — centrality computation could raise and the column would still report `""`. Now returns its error tuple like the other three helpers
+  - **Known limitation**: `include=["metric_errors"]` with no other metric names computes nothing, so the column is always `""` in that case — pass it alongside the metrics you want tracked, e.g. `include=["hop_count", "metric_errors"]`
+  - New `tests/export/test_distance_exporter_metric_errors.py`: 6 tests covering success, single/multiple failures, opt-out, the no-path-vs-error distinction, and default-schema stability; existing `tests/export/test_distance_exporter.py` updated for the new tuple return type
+  - Full `tests/export/` suite: 77 passed
+
+- **`ContextGraph.to_kg_dict()`: an adapter converting a `ContextGraph`'s internal `nodes`/`edges`/`source` shape into the canonical `entities`/`relationships`/`source_id` shape `RDFExporter` and `TemporalGraphQuery` consume** (#1081) by @cxzg007
+  - Previously there was no supported way to feed a `ContextGraph` into those consumers without hand-rolling the field remapping; `to_kg_dict()` does it once, with an `entities_only` option that drops relationships left dangling by the filter
+  - **Fixed during review** (Qodo): null `properties`/`metadata` on a node loaded from JSON raised `TypeError` when copied — both are now guarded with `or {}`; entity ids are coerced to `str(node_id)` to match `ContextEdge`'s already-str-coerced endpoints, so valid relationships were no longer dropped by `entities_only` filtering
+  - `RDFExporter`'s validator and `TemporalGraphQuery` now also accept `source_id`/`target_id` endpoints, the shape `to_kg_dict()` emits
+
+### Changed
+
+- **`GraphBuilder`'s 6 public methods now have Google-style docstrings** (#878, closes #876) by @cakeni
+  - `semantica/kg/graph_builder.py`'s `build`, `build_single_source`, `add_temporal_edge`, `create_temporal_snapshot`, `query_temporal`, and `load_from_neo4j` — the core knowledge-graph construction API, imported directly by callers — previously had zero docstrings across all 6 methods, the only file in a 10-file audit sample with that gap, despite CONTRIBUTING.md requiring Google-style `Args`/`Returns`/`Raises`/`Example` docs for public methods. Added full docstrings for all 6, plus the previously undocumented `build_single_source`, with runnable (`# doctest: +SKIP`) usage examples
+  - **Corrected during review**: `query_temporal`'s docstring claimed the query text was used to filter the graph; the implementation only records it in the result (`results = {"query": query, ...}`) with no interpretation or filtering. Corrected to state that explicitly
+  - **Corrected during review**: `create_temporal_snapshot`'s docstring implied entities were filtered for validity at the snapshot timestamp like relationships are; the implementation copies all entities unfiltered and only filters `relationships` by `valid_from`/`valid_until`. Docstring now distinguishes the two
+  - **Corrected during review**: `add_temporal_edge`/`create_temporal_snapshot` docstrings overclaimed numeric-timestamp support; `_parse_time()` only special-cases `str` and `datetime`, falling back to a bare `str()` cast for anything else (not true numeric parsing). Narrowed to "datetime or ISO-formatted string"
+  - **Fixed along the way**: `build()`'s `**options` documented a default only for `extract`; `extract_relations`, `extract_triplets`, `ner_method`, `relation_method`, and `triplet_method` all have concrete defaults in `_extract_from_text()` (`True`, `True`, `"llm"`, `"llm"`, `"llm"`) that were left unstated, inconsistent with CONTRIBUTING.md's own docstring example of noting defaults inline
+  - `python -m pytest tests/kg/test_kg.py tests/kg/test_graph_builder_external.py -q`: 45 passed
+- **`GraphBuilder` raw-text extraction now defaults to local extractors instead of LLM extraction** (#941, closes #930) by @dex0shubham
+  - `GraphBuilder._extract_from_text()` defaulted `ner_method`, `relation_method`, and `triplet_method` to `"llm"`, and ran relation extraction unconditionally (`extract_relations` defaulted to `True`) — all four contradicting the defaults documented in the `build()` docstring at the time (`"ml"` / `"pattern"` / `False`), and diverging from the standalone extractors (`NERExtractor` defaults to `method="ml"`, `RelationExtractor` and `TripletExtractor` to `method="pattern"`). The practical effect was that any raw-text `build()` call silently required a configured provider, an API key, and network access
+  - Defaults are now `ner_method="ml"`, `relation_method="pattern"`, `triplet_method="pattern"`, and `extract_relations=False`, matching the docstring. LLM extraction remains fully available and is now opt-in
+  - **To restore the previous behaviour**, pass the methods explicitly:
+    ```python
+    builder.build(
+        sources,
+        ner_method="llm",
+        relation_method="llm",
+        triplet_method="llm",
+        extract_relations=True,
+    )
+    ```
+  - #878 landed in the meantime and resolved the same mismatch in the opposite direction, documenting the LLM values (`"llm"` / `"llm"` / `"llm"`, `extract_relations: True`) as the contract. Per the decision on #930 the code is the side that changes, so those docstring defaults are corrected here to `"ml"` / `"pattern"` / `"pattern"` / `False`, keeping #878's formatting
+  - Removed the stale `# Default to LLM methods as per requirement` comment, which read as an intentional decision but did not match the documented contract
+  - **Fixed along the way**: `_extract_from_text()` constructed a fresh extractor for every text, and `NERExtractor.__init__` loads its spaCy model eagerly when the method includes `"ml"` — so with the new default, a multi-document build would have reloaded the model once per source. Extractors are now built once per `(kind, method)` and reused for the lifetime of the builder, via `GraphBuilder._get_extractor()`. This path was previously unreachable by default because the old `"llm"` default never touched spaCy
+  - **Fixed along the way**: `_extract_from_text()` never forwarded its extracted relations to triplet extraction — it passed only `entities=`, so `TripletExtractor` re-derived relations itself (via a method taken from `triplet_method`) whenever `relations is None`, duplicating work and producing triplets that could disagree with the relations already extracted using `relation_method`. Relations are now passed through as `relations=`; when relation extraction is disabled or fails, `None` is forwarded and `TripletExtractor` keeps its existing self-derivation behaviour
+  - **Fixed along the way**: `GraphBuilder._extraction_stats` was only initialised inside `build()`, so calling `_extract_from_text()` directly raised an `AttributeError` that the extraction path's broad `except` swallowed and reported as `"Entity extraction failed"`. It is now seeded in `__init__` as well; `build()` still resets it per run
+  - New regression coverage in `tests/kg/test_graph_builder_extraction_defaults.py` pinning all four defaults, verifying that no default resolves to `"llm"`, confirming explicit LLM opt-in still routes correctly, asserting extractors are constructed once across repeated texts, covering fallback method lists (e.g. `ner_method=["pattern", "ml"]`) for all three extractors, asserting relations are forwarded to triplet extraction (and that `None` is forwarded when relation extraction is disabled or fails), and running the real default path end to end with no provider mocked. Verified to fail against the pre-fix code
+  - Full `kg` suite: 473 passed
+
+- **Explorer graph canvas now renders edge labels** (#1013, closes #1009) by @yzxcj797
+  - `GraphCanvas.tsx` had no edge-label rendering path at all; Sigma's edge-label renderer draws `data.label`, but the graph state stored the relationship type under `edgeType`, so simply enabling the renderer would have left every edge blank. `graphSceneState`'s edge reducer now maps `edgeType` onto `label` (suppressed for hidden edges)
+  - Rendering is gated behind a new `edgeLabelsEnabled` entry in the Effects panel (default on), wired through the existing `GraphEffectToggle`/`GraphEffectsState` plumbing, so dense graphs can still turn labels off
+  - **Fixed during review** (Qodo): two follow-up passes closed gaps the first cut left — label rendering wasn't wired through `explorationEffectsPluginPhaseC.tsx`'s Phase C variant, and toggling the effect off mid-session didn't clear already-rendered labels
+  - New coverage in `explorer/tests/graphSceneState.display.test.ts`
+
+- **Removed `GraphWorkspaceShell.tsx`, `GraphRuntimeStage.tsx`, and `useGraphData.ts` — a second, unused implementation of the graph-loading/error-handling logic already fixed in `GraphWorkspace.tsx`** (#984, resolves the cleanup tracked in #981 by #980's review note) by @lakshayxi
+  - 1,564 lines removed; the surviving `GraphWorkspace` path is now the only implementation, so the "two copies that drifted apart" root cause #980 fixed can't recur in the copy nobody was maintaining
+
+- **Explorer README and `docs/explorer-setup.md` corrected to describe the authentication 0.6.5 actually shipped**, plus a documented `/ws/graph-updates` auth note (#1040, fixes #1028) by @Kyou12138
+  - Both docs still claimed the Explorer API had no built-in authentication after v0.6.5 added mandatory `SEMANTICA_API_KEY` enforcement with a `503` fail-closed default; corrected to describe the actual behavior, including that only protected routes require the key (`/api/health`/`/api/info` stay open), the non-loopback-bind CLI warning only fires in anonymous mode or when the key is unset, and `SEMANTICA_API_KEY`/`SEMANTICA_ALLOW_ANONYMOUS` are documented in the environment-variable table
+
+- **CI: pinned `github/codeql-action` to current v4** (#986) by @ZohaibHassan16, and **pinned Python dependencies in `requirements-ci.txt` for reproducible CI runs** (#945) by @yunaremaia, closing the gap where an unpinned CI dependency could silently change behavior between runs
+
+- **README now states up front that Semantica's explainability is system-level, not foundation-model-internal** (#1033, #1034) by @KaifAhmad1
+  - Nothing in the README previously scoped what "explainable" meant, leaving readers to assume Semantica could expose or reconstruct an LLM's internal reasoning. A callout now states explicitly that Semantica explains and audits what the AI *system* did — context fed in, decisions produced, provenance, relationships, policies applied — not the model's private internal reasoning, and moved the note near the top of the README rather than leaving it implicit
+
+### Fixed
+
+- **KG provenance tests asserted on generated ID strings instead of stored records, and `kg_provenance.py` was missed by the `utcnow` sweep** (closes #946) by @pravit-amp
+  - The KG workflow and integration suites checked that a tracker call returned an ID matching a prefix (`assert cent_id.startswith("centrality_")`) without ever reading the record back, so an ID generator that returned a well-formed string and wrote nothing would have passed. Worse, some of those calls named tracker methods that do not exist anywhere in `semantica/` (`track_layer_analysis`, `track_centrality_score`), so the assertions were satisfied with no real interaction behind them
+  - Those tests now read provenance back through `get_provenance()` and assert on algorithm metadata, and call the methods that actually persist records. Verified by mutation rather than by a green run alone: neutering the manager's storage write (`self.storage.store(...)` → no-op) fails 10 tests
+  - `GraphBuilderWithProvenance` in `semantica/kg/kg_provenance.py` still stamped `activity_started_at_time`/`activity_ended_at_time` with the deprecated `datetime.utcnow()`; it was outside the `export/`+`provenance/` scope of the #1114 sweep below and now uses the same `utc_now_iso()` helper. `docs/guides/provenance.md` and `docs/reference/provenance.md` were still documenting `utcnow()` and a naive timestamp example, and now show the helper and the offset-bearing form
+  - 16 tests across the affected suites ended in `return <value>` instead of asserting, which pytest reports as `PytestReturnNotNoneWarning`; now zero
+
+- **The temporal-evolution `stability` metric was a hardcoded placeholder, not a duration**
+  - `TemporalGraphQuery.analyze_evolution()` documents `stability` as a "relationship duration/stability measure", but the implementation appended a constant `1` for every relationship with both `valid_from` and `valid_until` set (`durations.append(1)  # Placeholder`). The reported stability was therefore always `1.0` when any bounded relationship existed and `0` otherwise — it never reflected how long relationships actually stayed valid, so it could not distinguish a graph of decade-long relationships from one of one-second relationships
+  - `stability` now computes the mean valid-time duration in seconds (`(valid_until - valid_from).total_seconds()`) across relationships that have both bounds set. Relationships with a missing or open `valid_from`/`valid_until` are skipped (their duration is unbounded), and non-positive intervals are clamped to `0`; an empty set still reports `0`
+  - New tests in `tests/kg/test_kg.py` assert the mean-duration result, the skipping of unbounded/half-open intervals, and the empty-graph zero case
+
+- **Every timestamp an export or a provenance record wrote was timezone-naive** (closes #1114) by @fabio-rovai
+  - `semantica/export/` stamped with `datetime.now().isoformat()`, which reads the machine's **local** clock; `semantica/provenance/` stamped with `datetime.utcnow().isoformat()`, which reads **UTC**. Both produce a naive value and both serialize identically, so nothing downstream can tell which zone a given timestamp belongs to — the same string means two different instants depending on which module wrote it
+  - In RDF the consequence is silent rather than loud. Under XSD 1.1 a value with no timezone compared against one with a timezone is indeterminate whenever the two fall inside the ±14 hour window; SPARQL turns an indeterminate comparison into an error, and `FILTER` discards errors as non-matches. A timezone-qualified query over an Oxigraph store returns an answer with every Semantica-written record quietly absent from it, which is a poor property for `prov:generatedAtTime`, `prov:startedAtTime`, `prov:endedAtTime` and `prov:atTime` to have
+  - New `utc_now()`/`utc_now_iso()` in `semantica/utils/helpers.py`, exported from `semantica.utils`, and used at all 29 call sites in `export/` (`json_exporter`, `yaml_exporter`, `report_generator`, `export_provenance`) and `provenance/` (`manager`, `schemas`, `bridge_axiom`). Values now read `2026-08-19T14:19:04.229937+00:00`: one unambiguous instant, comparable against any correctly stamped value, and valid `xsd:dateTimeStamp`. `sem:exportedAt`'s range in `semantica/ontology/vocabulary/semantica-ns.ttl` is tightened from `xsd:dateTime` accordingly, and its comment no longer has to explain why the weaker range was necessary
+  - `datetime.utcnow()` is deprecated as of Python 3.12 and scheduled for removal; constructing a `ProvenanceEntry` under `-W error::DeprecationWarning` on 3.13 raised, and no longer does
+  - New `tests/export/test_timestamp_timezones.py` and `tests/provenance/test_timestamp_timezones.py`: offset presence on every export and provenance path, PROV-O literals valid as `xsd:dateTimeStamp`, comparison against a timezone-aware instant without `TypeError`, the Oxigraph filter that dropped the naive value (with a bound inside the indeterminate window, so the test cannot pass by accident), and the document `@id` remaining a valid IRI with `+00:00` in it. 11 of the 13 fail on the parent commit
+  - **Fixed during review** (Qodo): once new entries carry `+00:00` and stored ones do not, `ProvenanceManager.query_recorded_between` and `audit_log` compared ISO timestamps as raw strings, so they ordered by spelling rather than by instant — an inclusive naive bound naming a stored offset-bearing timestamp sorted *below* it and dropped the record, and a bound written in another offset landed wherever its digits fell (`19:45+05:30` is 14:15Z, but sorted after 14:19Z). Both now compare instants through a new `to_utc_datetime()` helper that reads a missing offset as UTC, which is what the values written before this change actually were; a bound that cannot be read as a timestamp keeps the historical string comparison rather than raising on a call that used to work
+  - The remaining 147 naive call sites are in `context/`, `vector_store/`, `seed/` and elsewhere, where timestamps are compared against values parsed from previously stored naive strings. Converting those without a read-side migration would raise `TypeError: can't compare offset-naive and offset-aware datetimes` on existing data, so they are deliberately left for a separate change
+- **`SHACLGenerator` mangles `#`-terminated namespaces into `#/`, so generated shapes target nothing** (#1082) by @changshenhan
+  - `__init__` normalized `base_uri` with `rstrip("/") + "/"`, which turns `http://example.org/manufacturing#` into `...manufacturing#/` — the most common RDF namespace convention. Every generated URI (`sh:targetClass`, `sh:path`, shape URIs) then landed in a different namespace than the instance data, and SHACL validation silently passed because the shapes targeted nothing
+  - `__init__` now preserves a namespace already ending in `/` or `#`, matching the `#`-aware normalization `generate()` already applies; `shapes_uri` inherits the fix
+  - New `test_hash_namespace_base_uri_is_not_mangled` in `tests/ontology/test_ontology_advanced.py` fails on the pre-fix normalization and passes with it; full ontology suite (76 tests) green
+
+- **`split`/chunking paths bypassed the centralized spaCy model cache, reloading the model on every call** (#1042, closes #998) by @Accute9, reviewed by @Sameer6305
+  - `semantica/split/methods.py`'s `split_by_sentences()` and `semantica/split/semantic_chunker.py`'s `SemanticChunker.__init__` each called `spacy.load()` directly instead of reusing the process-level cache added in #889/`semantic_extract/methods.py`'s `load_spacy_model()` — every call/construction re-paid the ~120ms model-load cost independently of `NERExtractor`, which already used the cache
+  - Both now route through `load_spacy_model()`, sharing one cached `Language` instance per model name across `split_by_sentences()`, `SemanticChunker`, and `NERExtractor`; a missing model still falls back to regex/paragraph chunking without poisoning the cache for a later successful load
+  - **Fixed during review** (@Sameer6305): `NERExtractor.__init__()` still had a direct `spacy.load()` call site with the same cache-bypass issue, outside the two files named in #998 but sharing the same root cause; routed through the cache alongside stale test patch targets and a strengthened cache-configuration assertion
+  - **Fixed during review** (@KaifAhmad1): `SemanticChunker.__init__` only caught `OSError` around `load_spacy_model()`, while the sibling fix to `NERExtractor` in this same PR added a broader `except Exception` for a model that is installed but fails at runtime (e.g. a config incompatible with the installed spaCy version). A broken-but-present model crashed `SemanticChunker()` outright instead of degrading to fallback chunking like every other path in this PR. Added the matching `except Exception` branch, leaving `self.nlp` as `None`; new `test_semantic_chunker_falls_back_when_spacy_runtime_is_broken` mirrors the existing `NERExtractor` regression test for the same scenario
+  - New `tests/split/test_spacy_model_cache.py`: cache reuse across repeated calls/instances, shared cache between `split_by_sentences()`/`SemanticChunker`/`NERExtractor`, distinct model names loading separately, missing-model fallback without poisoning the cache, and the broken-runtime fallback added above
+  - `pytest tests/split/test_spacy_model_cache.py tests/split/test_splitter.py tests/split/test_chunkers.py`: all passing (3 pre-existing, unrelated `tests/test_ner_configurations.py` failures confirmed present on `main` before this PR)
+
+- **`export_yaml` raised a raw `AttributeError` on list input, silently wrote empty exports for unrecognized dict keys, and graph payloads were reconciled differently by every exporter** (#958, closes #956, #952, #953) by @pravit-amp, reviewed by @Sameer6305
+  - Graph payloads circulate under two vocabularies, `entities`/`relationships` and `nodes`/`edges`, and each exporter reconciled them locally with a different idiom — `LPGExporter` in particular dropped every entity whenever `nodes` was present but empty, the exact shape `JSONExporter` emits. A new `normalize_graph_payload()` in `utils/helpers.py` centralizes that decision once, adopted by `LPGExporter`, `ArangoAQLExporter`, `Neo4jCSVExporter`, and both YAML exporters; `ContextGraph.to_dict()` now round-trips through YAML correctly as a result
+  - `export_yaml(records, path)` on a bare list previously failed with `AttributeError` from inside the exporter; it and the other YAML methods now reject non-mapping input with an actionable `ProcessingError` naming the expected keys, since these formats distinguish entities/relationships/triplets and guessing which one a list represents would mislabel the records
+  - `export_yaml({"data": [...]}, path)` previously wrote a structurally valid file with every collection empty, no exception, no warning, and the progress log reporting a completed export. `export_semantic_network`, `export_for_pipeline`, and `export_ontology_schema` now raise `ValidationError` when the payload shares no recognized key with what the method reads, or resolves to nothing while an unread key still holds records — an empty mapping is still accepted, since a genuinely empty graph has no records to lose
+  - **Breaking**: the two cases above, plus a bare list, now raise instead of returning cleanly with data silently dropped or a raw `AttributeError` from exporter internals. Migration: pass records under a recognized key (`{"entities": [...]}` / `{"nodes": [...]}` for `semantic_network`, `{"classes": [...]}` for `schema`)
+  - **Fixed during review** (Qodo): progress tracking could report a completed export before the output directory existed or the file was written; `export()` now creates the directory and serializes before starting tracking, so a rejected export leaves nothing behind
+  - **Fixed during review** (@Sameer6305, round 1): `normalize_graph_payload()`'s collection resolver treated any truthy value as a collection — `{"entities": "abc"}` silently became three single-character records, `{"entities": 42}` leaked a raw `TypeError` from inside `list()`. Collection values are now validated before conversion, rejecting strings/bytes/mappings/non-iterable scalars by name. Separately, `Neo4jCSVExporter._normalize_graph` called the shared resolver with `require_recognized=False`, so it alone kept accepting an unrecognized mapping as a silent empty export; the opt-out (introduced earlier in this same PR, with no other caller) was removed
+  - **Fixed during review** (@Sameer6305, round 2): `YAMLSchemaExporter`'s usable-schema check could treat scalar schema metadata (`version`, `uri`, `title`, `description`) as evidence records had been exported, letting records under an unread key drop silently; and `_is_record()` accepted modules and class/type objects through the generic `__dict__` path, which would have reached exporter internals instead of failing at the boundary. Both closed, with regression coverage
+  - **Fixed during final maintainer review** (before merge): four more gaps in the shared boundary that the earlier rounds didn't reach
+    - `LPGExporter`/`ArangoAQLExporter` called `normalize_graph_payload()` with no type guard, so non-mapping input raised `ValidationError` from inside the resolver — while YAML and `Neo4jCSVExporter` raised `ProcessingError` for the identical mistake, per this PR's own stated contract. The `_require_mapping()` guard that already existed in `yaml_exporter.py` is now shared from `utils/helpers.py` and used by all three
+    - `Neo4jCSVExporter._normalize_graph` checked `isinstance(graph, dict)`, so a non-dict `Mapping` (`MappingProxyType`, `ChainMap`) fell through to the object-attribute branch and was rejected, even though the identical payload exported fine via `LPGExporter`/`ArangoAQLExporter`/YAML. Now checks `isinstance(graph, Mapping)`
+    - `normalize_graph_payload()` accepts dataclass and attribute-bearing object records (`Neo4jCSVExporter._record_to_dict` reads them), but `LPGExporter`/`ArangoAQLExporter` call `.get(...)` directly on resolved entities — an object-shaped record passed validation only to crash with a raw `AttributeError` once used, the exact failure this PR's boundary exists to prevent. Records are now converted to plain dicts at the boundary (`_coerce_records` → new `_record_to_dict`), so every consumer gets a uniform shape regardless of which reading the caller used
+    - Two non-empty spellings of the same collection (e.g. `entities` and `nodes`) holding identical records in a different order were rejected as conflicting, since the check used plain list equality; a caller round-tripping through a dict-keyed cache or a set has no reason to preserve order. Comparison is now an order-independent multiset of each record's canonical JSON form
+  - New regression coverage in `tests/utils/test_normalize_graph_payload.py`: exception-type parity for non-mapping input across `export_lpg`/`export_arango`/`export_neo4j_csv`, dataclass-record conversion verified end-to-end through the same three exporters, `Neo4jCSVExporter` accepting a `MappingProxyType` payload, and reordered-alias equality (plus a duplicate-count case confirming the multiset check still catches real conflicts); 4 existing tests updated to assert the corrected dict-conversion behavior instead of the previous object passthrough
+  - `pytest tests/export tests/utils tests/context tests/test_export_module.py tests/test_export_methods_wrapper.py tests/test_notebooks_simulation.py`: 718 passed, 4 skipped (up from 641 passed, 62 subtests at PR submission); `black`/`isort`/`flake8 --max-line-length=88` clean on every line this PR touches; `python -m build`: succeeds
+
+- **`ContextGraph.add_edge` had no dedupe — identical edges were stored repeatedly under one shared edge ID, and re-ingest doubled the edge set** (#926, closes #922) by @pravit-amp
+  - `_add_internal_edge` appended to `self.edges`, `edge_type_index`, and `_adjacency` unconditionally, with no check for an edge already present. Edge identity is content-derived (`_resolve_edge_identity` builds `edge_id` from `source_id`/`target_id`/`edge_type`/`weight`/`metadata`/`valid_from`/`valid_until`), so two identical `add_edge` calls produced two edge objects sharing one `edge_id` — the graph already considered them the same edge, it just kept both copies. `self.nodes` already deduped by ID; edges did not, so `stats()["edge_count"]` inflated, `density()` could exceed its mathematical maximum of `1.0`, and a refresh/restore job calling `build_from_entities_and_relationships()` (or reloading a saved graph) doubled the edge set on every cycle
+  - Added an `edge_id -> ContextEdge` index (`_edge_index`), mirroring how `self.nodes` dedupes by node ID. `_add_internal_edge` now returns `False` when the `edge_id` already exists, checked before touching `edges`/`edge_type_index`/`_adjacency` and before firing the mutation callback, so a repeat `add_edge` is a silent no-op with no phantom `ADD_EDGE` audit event
+  - Genuinely parallel edges are unaffected: differing type/weight/metadata/validity still produce distinct content-derived `edge_id`s, so multigraph semantics are preserved
+  - Both state-reset paths (`load_from_file()` and `clear()`) also clear `_edge_index`
+  - New tests: repeat `add_edge` is a no-op, parallel edges with distinct attributes are preserved, re-ingest via `build_from_entities_and_relationships()` stays at one edge, and `clear()` resets the dedupe index
+  - `pytest tests/context/test_context.py`: 31 passed
+
+- **`POST /api/enrich/extract` returned 503 on every request; the whole `/api/decisions*` family returned 500 as soon as a decision existed** (#886, closes #883, closes #884, closes #889) by @joseedson18jc, reviewed by @Sameer6305
+  - `semantica/explorer/routes/enrich.py` imported `extract_entities`/`extract_relations` from `semantica.semantic_extract.methods`, names that module never defined (only per-strategy variants like `extract_entities_ml` exist) — the `except ImportError` handler reported this as `"semantic_extract module not available"`, masking a wiring bug as a missing dependency. The route now calls `NamedEntityRecognizer`/`RelationExtractor` directly and forwards extracted entities into relation extraction instead of re-deriving them
+  - `ContextGraph.record_decision()` stores `timestamp` as `datetime.now().timestamp()` (a float), while `DecisionResponse.timestamp` was typed `Optional[str]`; passing the value through unconverted failed pydantic validation on every decision route (`/api/decisions`, `/{id}`, `/{id}/chain`, `/{id}/precedents`, `/{id}/compliance`). Added a `field_validator(mode="before")` on `DecisionResponse` normalizing float/int/datetime inputs to ISO-8601
+  - Folds in the fix for #889: `extract_entities_ml`/`extract_relations_similarity`/`extract_relations_dependency` called `spacy.load()` on every invocation (~120ms of a ~132ms call, ~60x the actual extraction work). Added a process-level, lock-guarded `load_spacy_model()` cache in `semantic_extract/methods.py`, keyed by model name; failed loads are not cached, and the separate `get_nlp_model()` cache (different `disable=` pipeline config for similarity work) is kept independent to avoid handing one caller's spaCy pipeline to another
+  - **Fixed during review** (@Sameer6305): capped previously-unbounded input text on `/api/enrich/extract`; tightened the route's exception handling
+  - **Fixed during review** (@KaifAhmad1): the timestamp validator's `math.isfinite()` guard only rejected NaN/inf — a finite-but-out-of-range epoch (e.g. milliseconds mistakenly stored instead of seconds, such as `1723600000000`) still raised an uncaught `OverflowError`/`OSError` from `datetime.fromtimestamp()`, reintroducing an unhandled 500 on `/api/decisions*` for exactly the class of bug this PR closes. Now caught and re-raised as a `ValueError`. Also excluded `bool` from the numeric branch (`isinstance(True, int)` is `True` in Python, so `timestamp=True` was silently coerced to epoch 1 instead of being rejected)
+  - New/updated tests: `tests/explorer/test_explorer_api.py` (`TestRecordedDecisions`, extraction coverage, 4 new `TestDecisionResponseTimestampValidator` cases for the range/bool fixes), `tests/semantic_extract/test_spacy_model_cache.py` (6 tests)
+  - `pytest tests/explorer tests/semantic_extract/test_spacy_model_cache.py`: 266 passed
+
+- **Explorer UI hid backend failures: graph load hung forever, landing page always showed "System Online"** (#980, closes #977) by @ZohaibHassan16, reviewed by @Sameer6305
+  - `GraphWorkspace.tsx` only destructured `{ data, isLoading, isFetching }` from `useLoadGraph()`, ignoring the `isError`/`error`/`refetch` that `useQuery` (`retry: 0`) already returned. Combined with `GraphLoadingOverlay` having no error prop and `showLoadingOverlay` staying true whenever `loadingProgress` held a stale frame, a backend-down or failed fetch left the graph workspace stuck on the last progress frame indefinitely, with no error message and no way to recover short of a full page reload
+  - `GraphLoadingOverlay` now accepts `error`/`onRetry` and renders an error card with the real fetch error message and a Retry button (`refetch()`) instead of the stuck progress UI
+  - The landing page's `WelcomeScreen` replaced its hardcoded `ready: boolean` (and hardcoded "System Online" text) with a real `checking` / `online` / `offline` status derived from the same connectivity probe already driving the 4th metric card, so the status dot, text, and metric can no longer drift apart or lie about connectivity
+  - **Smaller fixes bundled in the same PR**: search results are now dismissible (previously stayed open indefinitely, pushing the graph down); relevance scores display as rounded whole numbers instead of `96.900`/`138.000`; added a debounced (250ms) typeahead combobox to graph search with arrow-key navigation, `aria-activedescendant`, and Escape-to-close, using the existing `/api/graph/search` endpoint
+  - **Fixed during review** (Qodo): the typeahead's debounced fetch had no `AbortController`, so a fast-typing user could have a stale suggestion response resolve after a newer one, replacing correct suggestions with outdated ones. In-flight requests are now aborted on every re-debounce and when the query is cleared after a selection
+  - **Noted during review** (@Sameer6305): `GraphWorkspaceShell.tsx` contains a third, unused implementation of the same graph-loading/error-handling logic this PR fixes — the issue itself named "two copies that drifted apart" as the root cause the original bug slipped through. Deliberately left out of this PR's scope and tracked separately in #981 rather than blocking this fix
+  - `npx tsc -b`: clean; `test:graph-store`/`test:graph-workspace`/`test:plugin-registry`: 42 passed; `npm run build`: succeeds
+
+- **Markdown import hardened against TOCTOU symlink races during file reads** (#932, closes #856) by @lakshanmuruganandam, with fixes by @Sameer6305
+  - `AgentMemory._read_markdown_path` read files via `Path.read_text()` after a `Path.is_symlink()` pre-check, leaving a time-of-check/time-of-use window: a path validated as a regular file could be swapped for a symlink before the actual read, causing the importer to follow the link and read an unintended target
+  - Reads now go through a new `_read_markdown_file_content()` helper: the path is opened via low-level `os.open()` with `os.O_NOFOLLOW` on platforms that support it (POSIX), so a symlink substituted after validation fails atomically with `ELOOP` instead of being followed; the resulting file descriptor is then verified with `os.fstat()`/`stat.S_ISREG()` to reject non-regular files (FIFOs, devices) even after a successful open
+  - Directory imports now also exclude symlinked entries from the file listing (`not file_path.is_symlink()`), consistent with the single-file path already rejecting them
+  - **Known limitation**: Windows has no `os.O_NOFOLLOW`, so on that platform the only defense is the earlier `is_symlink()` pre-check, leaving a narrow TOCTOU window; documented inline rather than implying a stronger cross-platform guarantee than the implementation provides
+  - New `tests/context/test_agent_memory_markdown.py` coverage: rejecting a symlinked path at both the private helper and the public `import_data()` API, silently excluding symlinked entries during directory import, and the `fstat()`/`S_ISREG` guard against non-regular files (mocked FIFO)
+  - `pytest tests/context/test_agent_memory_markdown.py`: 46 passed, 4 skipped (symlink-creation tests skip on Windows without `SeCreateSymbolicLinkPrivilege`)
+
+- **`VectorManager.maintain_store()`/`collect_statistics()` crashed with `AttributeError` on persistent `VectorStore` backends** (#914, closes #855) by @yunaremaia, with fixes by @Sameer6305
+  - Both methods accessed `store.vectors`/`store.metadata` directly, which are only initialized for the `inmemory` backend — any persistent backend (FAISS, Qdrant, Pinecone, Milvus, SQLite, PgVector, Weaviate) crashed immediately. Same root cause as the #839/#843/#845/#848 cluster, but `VectorManager` operates on a `VectorStore` instance from the outside, so the fix needed a public accessor rather than another internal guard
+  - Added a backend-agnostic `VectorStore.count()`: the `inmemory` backend counts its local dict; persistent backends delegate to a `count()` on the wrapped backend store when one exists, or raise `NotImplementedError` — following the `get_vector()`/`get_metadata()` precedent from #843, a missing/uninitialized backend store is never silently reported as an empty, healthy store
+  - `maintain_store()` and `collect_statistics()` now go through `store.count()` instead of touching `.vectors`/`.metadata`
+  - **Fixed during review** (@Sameer6305): the initial version had `count()` implemented at the dispatch level only, with no shipped backend actually providing one, and `maintain_store()` manufactured a vacuous `metadata_count == vector_count` tautology for persistent backends (always reporting `healthy: True` without checking anything). Added real `count()` implementations to `FAISSStore` (`len(index.vector_ids)` — FAISS has no delete path, so this list is always consistent with the index), `SQLiteVecStore`, and `PgVectorStore` (both via `SELECT COUNT(*)`); `Qdrant`/`Pinecone`/`Milvus`/`Weaviate` continue to raise `NotImplementedError` since none of them guarantee a cheap, reliable synchronous count. `maintain_store()` now reports `metadata_count: None` for persistent backends instead of the fabricated equality, with `healthy` meaning "store is reachable," not "metadata verified"
+  - Two earlier Qodo findings (a count() path that silently returned 0 for a missing backend store, and an unvalidated `hasattr` check that could raise `TypeError` on a mis-shaped adapter) were fixed before this review — replaced with `NotImplementedError` and a `getattr`+`callable()` capability check, respectively
+  - New `tests/vector_store/test_vector_manager_persistent.py`: dispatch-level tests for `count()` (inmemory, delegation, missing backend, non-callable `count`, mis-shaped adapter), full `VectorManager` inmemory semantics including divergence detection, persistent-backend dispatch tests, and backend-specific tests against real/mocked FAISS, SQLite (`sqlite-vec`, skipped if unavailable), and PgVector stores
+  - Core `vector_store` suite: 40 passed
+
+- **`ContextGraph.get_node_property`/`get_node_attributes` "not found" contract clarified; `add_node_attribute` mutation-callback exception safety fixed** (#882, closes #877) by @ZohaibHassan16
+  - `get_node_property` returned `None` for both "node missing" and "property missing" with no way to distinguish them, and `get_node_attributes` returned `{}` for a missing node while its siblings disagreed on the not-found signal (`get_node_property`/`find_node` → `None`, `get_edge_data` → `{}`). Both now accept a `default=` parameter matching `dict.get()`'s convention, defaulting to their historical return values (`None` and `{}` respectively) for backward compatibility. Callers that need to disambiguate "node missing" from "value legitimately absent" can pass a private sentinel as `default`
+  - Added Google-style docstrings to `get_node_property`, `get_node_attributes`, `get_edge_data`, and `find_node` documenting each method's not-found contract, addressing #877's "sibling not-found contract undocumented" gap
+  - **Corrected during review**: the PR as submitted claimed to fix `add_node_attribute` firing its `mutation_callback` "outside `with self._lock`, without holding the lock," but the diff only removed a stray blank line — the callback call remained outside the lock, unchanged. Further investigation found this was not actually a bug: `self._lock` is a `threading.RLock`, and the same release-the-lock-before-invoking-the-callback pattern is used deliberately in `_add_internal_node`/`_add_internal_edge` elsewhere in this class, avoiding holding the lock for the duration of an arbitrary user-supplied callback. The real inconsistency was that, unlike those two siblings, `add_node_attribute`'s callback call wasn't wrapped in `try/except` — a raising callback propagated uncaught here but was caught and logged there. Now wrapped the same way (`except Exception as e: self.logger.warning(...)`)
+  - 13 tests covering happy path, missing node, missing property, sentinel disambiguation, falsy-zero, callback firing/non-firing, and (added during review) a raising callback no longer propagating out of `add_node_attribute`
+  - `pytest tests/context/test_context.py -q`: 27 passed
+
+- **Three `tests/normalize/` tests failed for reasons unrelated to the normalize implementations: a missing optional-dependency skip guard, an incomplete chardet allowlist, and a UTC/local timezone mismatch** (#881, closes #860) by @aoright
+  - `test_detect_language`/`test_detect_with_confidence` in `tests/normalize/test_language_detector.py` asserted on real `langdetect` output with no skip guard, even though `langdetect` is an optional dependency absent from `pyproject.toml` that `LanguageDetector` already degrades gracefully without (`LANGDETECT_AVAILABLE = False`, falls back to `default_language`) — any environment without it failed both tests unconditionally, including a fresh CI run without optional extras installed. Both are now gated with `@unittest.skipUnless(LANGDETECT_AVAILABLE, ...)`
+  - `test_detect_encoding` in `tests/normalize/test_encoding_handler.py` asserted `chardet.detect()`'s result against a 3-name allowlist (`iso-8859-1`/`windows-1252`/`latin-1`); on a short Latin-1 sample, chardet is free to return other compatible single-byte codepages (e.g. `windows-1253`), which fails the allowlist and then cascades into `test_convert_to_utf8` decoding the bytes as Greek instead of the original text. The test now uses a longer, unambiguous Latin-1 corpus and asserts that the detected encoding round-trip-decodes the original text instead of matching a fixed name list; `test_convert_to_utf8` now passes `source_encoding="latin-1"` explicitly rather than relying on chardet's heuristic auto-detection
+  - `test_normalize_date_relative` in `tests/normalize/test_date_normalizer.py` compared `RelativeDateProcessor`'s local-clock-based `"today"` (`datetime.now()`, naive, UTC-normalized after the fact by `convert_to_utc()`) against a separately-computed UTC reference date — failing intermittently in any timezone east of UTC whenever the local and UTC dates diverge for part of the day. The test now patches `datetime.now()` to a fixed reference time, making the assertion independent of host timezone
+  - `pytest tests/normalize`: 77 passed, 2 skipped (`langdetect` not installed); `black`/`isort`/`flake8 --max-line-length=88` clean on all three changed files. Test-only change; no production code touched
+
+- **MCP server reported a stale `0.4.0` version instead of the installed package version** (#870, closes #863) by @oiahoon
+  - `semantica/mcp_server/__init__.py` hardcoded `"version": "0.4.0"` in both the MCP `initialize` response (`SERVER_INFO`) and the `semantica://schema/info` resource, regardless of the actual installed `semantica` version — every MCP client (Claude Desktop, Windsurf, Cline, Continue, VS Code Copilot, etc.) showed the wrong server version. Both surfaces now derive from `semantica.__version__`, the package's authoritative version source, so they can no longer drift from `pyproject.toml`
+  - New regression coverage in `tests/test_mcp_server_version.py`, including `!= "0.4.0"` canaries and a cross-surface consistency check
+  - **Fixed along the way**: the separate root-level `mcp/` package (`mcp/__init__.py`, `mcp/server.py`, `mcp/resources/registry.py`) — a companion MCP server implementation not included in the built distribution, but documented in `mcp/__init__.py` as a supported way to run against Claude Desktop/Windsurf/etc. from a source checkout — had the same three hardcoded `0.4.0` literals; fixed the same way, with matching regression tests in `tests/test_mcp_package_version.py`
+
+- **`VectorStore._filter_by_metadata()` `AttributeError` on all persistent backends** (#857, closes #849) by @TaherTadpatri
+  - `_filter_by_metadata()` iterated `self.metadata` directly, which only exists on the `inmemory` backend — any persistent backend (`faiss`, `qdrant`, `pinecone`, `milvus`, `pgvector`, `sqlite`, `weaviate`) crashed with `AttributeError` on `filter_decisions(query=None, ...)` / metadata-only filtering. Filtering is now delegated to a native `filter_by_metadata()` implemented on each backend store, using backend-native payload/SQL/JSON filtering (Qdrant `scroll()`, Pinecone `query()`, Milvus expression filters, PostgreSQL JSONB, SQLite `json_extract()`, Weaviate collection filters)
+  - **Fixed along the way**: `PineconeStore.get_index()` and `filter_by_metadata()` called a nonexistent `self.describe_index_stats()` on the store itself (the method only exists on the `PineconeIndex` wrapper returned by `self.index`); the resulting `AttributeError` was silently swallowed, so dimension auto-detection always failed quietly. Now correctly calls `self.index.describe_index_stats()`
+  - **Fixed along the way**: `PineconeStore.filter_by_metadata()` probed for filter-only matches using an all-zero dummy query vector, which Pinecone rejects for cosine-metric indexes — the library's own default — making metadata-only filtering silently non-functional out of the box. Now uses a unit vector instead
+  - **Fixed along the way**: `PgVectorStore.filter_by_metadata()`'s list-filter branch formatted boolean values with `str(v)` (`'True'`/`'False'`), never matching PostgreSQL JSONB's lowercase `'true'`/`'false'` text rendering, even though the equivalent scalar-filter branch already handled this correctly
+  - **Fixed along the way**: list-valued metadata fields (e.g. `{"tags": ["python", "js"]}`) could never match a list filter on the SQLite or PostgreSQL backends, because both extracted the whole array as its JSON/text representation instead of matching individual elements — silently diverging from the in-memory backend's set-intersection semantics. SQLite now uses `json_each()` over a `json_type`-guarded array/scalar wrapper; PostgreSQL now uses the `?|` "any array element" operator alongside the existing scalar `= ANY(...)` path
+  - **Fixed along the way**: `FAISSStore.filter_by_metadata(limit=0)` returned one result instead of zero, because the limit check ran after appending the current match
+  - **Fixed along the way**: `MilvusStore`'s metadata expression builder rendered `NaN`/`Infinity` filter values as bare unquoted tokens, producing an invalid Milvus expression whose server-side rejection was then swallowed by a broad `except`, indistinguishable from "no matches"; these values are now rejected up front with a clear `ValidationError`
+  - New/expanded test coverage in `tests/vector_store/test_backend_metadata_filtering.py` (all 7 backends, including the Pinecone dimension/zero-vector, PgVector boolean-list, FAISS `limit=0`, and Milvus `NaN` regressions) and `tests/vector_store/test_sqlite_vec_store.py` (new `TestSQLiteVecStoreFilterByMetadata`, run against the real `sqlite-vec` extension, including the array-vs-scalar intersection case)
+
+- **`DistanceExporter` silently swallowed metric computation failures, exporting `None` values indistinguishable from a legitimate "no path" result** (#879, closes #874) by @AmirF194
+  - `_betweenness`, `_hop_distance`, `_weighted_distance`, and `_semantic_similarity` each caught `Exception` and returned their sentinel (`None`/`{}`) with no logging; a failed computation and a real "no path exists" looked identical in exported CSV/JSONL/DataFrame data. All four now log a `warning` with `exc_info=True` before returning the sentinel; exported row shape and values are unchanged
+  - **Fixed along the way**: the module logger was built with `get_logger(__name__)`, which double-prefixed it to `semantica.semantica.export.distance_exporter` — a name `setup_logging()` never configures — so this module's logging (including a pre-existing `logger.debug` call) was silent regardless. Now uses `get_logger("export.distance_exporter")`, matching every other exporter in the module
+  - New regression coverage in `tests/export/test_distance_exporter.py`: warnings fire on exception for all four helpers, exported sentinel values/shape stay unchanged, and the legitimate "no KG backend" `None` path still logs nothing
+  - Full `tests/export/` suite: 71 passed
+
+- **`explain_violations` rendered hardcoded placeholders (`min_count=1`, `max_count=1`) instead of the SHACL shape's real constraint values, and misused the violation message text as the datatype/class value** (#1094) by @cxzg007
+  - `_run_pyshacl` never read `sh:minCount`/`sh:maxCount`/`sh:datatype`/`sh:class` back from the violation's `sh:sourceShape`, so every plain-English explanation was wrong regardless of what the shape actually declared. `SHACLViolation` now carries those four fields (also exposed via `to_dict()`), populated by back-referencing `sh:sourceShape`; `explain_violations` renders the real values, falling back to `"?"` when a value is genuinely absent
+  - **Known limitation**: `sh:qualifiedMinCount`/`sh:qualifiedMaxCount` are not handled yet and still fall back to the `"?"` placeholder
+  - New regression tests cover both the rendering path and the `sh:sourceShape` back-reference (skipped when `pyshacl`/`rdflib` are absent)
+
+- **Entity merging silently dropped `entity_id` aliases, and exact-match entity resolution had three correctness gaps** (#1086, #1026) by @T1mn
+  - `entity_merger.py`/`merge_strategy.py`/`entity_resolver.py` used inconsistent logic for extracting an entity's id across the merge path, so a merged entity could lose the `entity_id` aliases that let later lookups find it under its old identity. A new `semantica/utils/entity_ids.py` unifies id extraction across all three call sites
+  - `EntityResolver`'s exact-match path is now honored rather than silently falling through to fuzzy matching in some cases; entities with no identifier are preserved instead of being dropped, and blank exact-match names are ignored rather than matching every other blank name
+  - New/expanded coverage in `tests/kg/test_entity_pipeline.py` and `tests/kg/test_entity_resolver_exact.py`
+
+- **`flatten_dict()` silently collided keys when a flattened path from one branch matched a literal key already present at the target depth** (#1062) by @shahzaib-ahmadcs
+  - Two differently-shaped inputs could flatten to the same output key, with the second write silently overwriting the first — no error, no warning, just a dropped value. Collisions are now detected and handled explicitly instead of overwriting
+
+- **`ExcelParser.__init__` raised `NameError` on every instantiation — `get_progress_tracker()` was called but never imported** (#1016, closes #1014) by @pravit-amp
+  - Same defect as the one fixed for `SimilarityCalculator` in #530, this time in `semantica/parse/excel_parser.py`; the existing test imported the class but never constructed it, so nothing caught the missing import. Added construction coverage for every parser exported from `semantica.parse`, driven off `__all__` so future additions are covered automatically, living outside `test_parse_comprehensive.py` (whose `setUp` mocks `get_progress_tracker` into each module and would mock away the exact interaction under test)
+
+- **Graph analytics (`centrality_calculator.py`, `community_detector.py`, `connectivity_analyzer.py`) dropped isolated nodes and diverged on how each computed its working view of the graph** (#1011) by @T1mn
+  - Each analyzer had its own ad hoc logic for building the node/edge set it operated over, and none of them included nodes with no edges — a node with zero connections simply vanished from centrality scores, community assignments, and connectivity reports instead of appearing with a zero/singleton value. A new shared `semantica/kg/_graph_view.py` centralizes graph-view construction (including node fallbacks and community payload shaping) for all three analyzers, which are now ~250 lines lighter combined
+  - New `tests/kg/test_analytics_node_scope.py` covering isolated-node presence across all three analyzers
+
+- **Explorer fired temporal-bounds and snapshot requests before the graph itself had loaded, tripling failed requests when the backend was down and leaving the timeline scrubber with nothing to scrub** (#1003) by @lakshayxi
+  - Two new predicate functions gate the temporal effects on the graph having actually loaded (an empty graph still counts as loaded); confirmed against a downed backend that this cuts three failing requests per page load down to one
+
+- **`SeedDataManager.load_from_database()` never actually reached the database, and connection failures were mislabeled as a missing optional dependency** (#995, closes #973) by @yzxcj797
+  - `DBIngestor.execute_query`/`export_table` need the connection string as their first positional argument; `load_from_database()` only passed it into the constructor's config dict, which those methods never read, so every call raised `TypeError` before connecting. Also split the combined `except (ImportError, OSError)` handling apart — a genuine connection failure was reported as `"module not available"`, sending debugging in the wrong direction; `OSError` now propagates as an actual failure, chained via `from e`
+
+- **SPARQL `CONSTRUCT` detection matched inside a leading `#`-comment, misclassifying `SELECT`/`ASK` queries as `CONSTRUCT` across all four SPARQL backends** (#951) by @pravit-amp
+  - `CONSTRUCT_QUERY_RE` skipped comments with a bare `\#[^\n]*`, whose backtracking `*` let a `# CONSTRUCT ...` comment line "swallow" the real query-form keyword on the next line for a query like `# CONSTRUCT ...\nSELECT ...`. The mistaken `CONSTRUCT` classification sent `Accept: text/turtle` and tried to parse a SELECT/ASK response body as Turtle, failing with a misleading parse error. The regex now requires a comment to reach a line terminator (LF or CR, per the SPARQL grammar) before matching
+
+- **`k_shortest_paths` mutated caller-visible graph state during traversal and ignored direction when excluding already-used edges** (#1000) by @T1mn
+  - `semantica/kg/path_finder.py`'s search left side effects behind after returning, and edge exclusion during Yen's-algorithm-style path removal didn't respect the traversal direction of directed graphs, letting a later search see edges that should have been available. Both fixed; new coverage in `tests/kg/test_path_finder.py`
+
+- **`trace_decision_causality()` ignored explicitly recorded causal edges, inferring causes only from shared NER entities plus timestamp ordering** (#983) by @hsd2514
+  - A `CAUSED`/`INFLUENCED`/`PRECEDENT_FOR` edge added via `add_causal_relationship()` had no effect on the trace — when entity extraction found nothing in common between two decisions, `trace_decision_chain()` came back empty even with an explicit edge stored in the graph. Explicit causal edges are now traversed first as ground truth, with entity/timestamp inference kept as an additive fallback for pairs with no explicit link; edges whose source has no decision record (e.g. a graph restored via `from_dict`) are skipped so a stale edge can't abort the trace
+
+- **`RepoIngestor`'s module-level DNS resolve cache had no lock, raising `RuntimeError: OrderedDict mutated during iteration` under concurrent `ingest_repository()` calls** (#979) by @manjunathbhaskar
+  - `_REPO_HOST_RESOLVE_CACHE` is a shared `OrderedDict` read, written, and pruned by every thread with no synchronization — reliably reproduced with 32 threads hammering resolution under a low TTL and small cache cap. Now guarded by a lock
+
+- **`GraphBuilder` didn't remap relationship endpoints after entity resolution merged nodes, leaving relationships pointing at ids that no longer existed in the resolved graph** (#978) by @T1mn
+  - New coverage in `tests/kg/test_graph_builder_external.py`; a follow-up commit hardens the remapping against edge cases found during review
+
+- **Explorer's dev server esbuild target didn't match the browser targets the production build declares**, occasionally producing dev-only syntax errors on older browsers (#966) by @le-czs
+  - `explorer/vite.config.ts` now sets the dev esbuild target explicitly to match
+
+- **`normalize`'s number normalizer accepted currency symbols without validating them against the surrounding text, and an earlier fix's currency-code matching wasn't token-bounded** (#940) by @Mr-Neutr0n, reviewed by @ZohaibHassan16
+  - Symbol currencies are now validated before being accepted; currency codes are matched on token boundaries so a code embedded inside a longer token no longer false-positives
+
+- **`ContextGraph.to_dict()` was the one reader on the class that didn't hold `self._lock`, raising `RuntimeError: dictionary changed size during iteration` under a concurrent writer and risking a torn snapshot otherwise** (#929) by @pravit-amp
+  - Every other reader (`stats()`, `density()`, `find_nodes()`, `find_edges()`, `get_neighbors()`, `get_nodes_by_label()`, `state_at()`, `save_to_file()`) already took the lock after it was introduced; `to_dict()` predated that change and was missed. `save_to_file()` was safe only incidentally, since it builds its payload inline under its own lock rather than delegating to `to_dict()`
+
+- **`PipelineWithProvenance` had a broken import and no working `run()` method** (#862) by @Karunasagar12
+  - `from .pipeline import Pipeline` failed because `Pipeline` lives in `pipeline_builder.py`, not a nonexistent `pipeline.py` — fixed to `from .pipeline_builder import Pipeline`. The class also had no `run()`; it now delegates to `ExecutionEngine.execute_pipeline()`, the intended execution path for a built `Pipeline`. The constructor now accepts a built `Pipeline` instance directly
+
+### Security
+
+- **Tarball restore path traversal, latent SQL injection, DNS-rebinding TOCTOU in the shared SSRF guard, stored XSS in report generation, and unvalidated SPARQL object IRIs in AnzoStore** (#1079) by @KaifAhmad1
+  - `semantica backup restore`'s tar extraction (`cli.py`) stripped only the literal `semantica-backup/` prefix and called `tar.extract()` with no path-containment check, no symlink/hardlink validation, and (on Python <3.12) no extraction filter — a crafted archive member (`../../<file>`, or a symlink pointing outside the restore root) could write arbitrary files above the restore directory. Every member is now validated for resolved-path containment before extraction, symlink/hardlink targets are rejected both lexically (absolute path, `..` segments) and by resolution, and `filter="data"` is applied on Python ≥3.12
+  - `DataExporter.export_table_data()` (`db_ingestor.py`) was missing the `text` import from `sqlalchemy` — a `NameError` that made the method non-functional, but latently: the query it built from raw f-string interpolation of `table_name`/`schema`/`where`/`order_by` was already injectable, so fixing the import alone (without also fixing the injection) would have silently armed it. Both are fixed together: the import is restored, `table_name`/`schema` are now validated against a strict identifier allowlist, and `where`/`order_by` are checked against a blocklist (statement separators, comments, UNION, DDL/DML keywords, time-based blind-injection primitives, schema-enumeration terms). This is a blocklist, not a grammar — it closes the concrete UNION-exfiltration path and common injection primitives, but a boolean-blind subquery using none of the blocked keywords could still get through; `where`/`order_by` must be treated as trusted/operator input, not exposed to untrusted end users, and the docstrings now say so explicitly
+  - `request_with_ssrf_guard()` (`ssrf.py`) validated a hostname's resolved IPs, then let the underlying HTTP client re-resolve the same hostname independently at connect time — a low-TTL or DNS-rebinding answer could differ between the two lookups, so a hostname that validated as public could still connect to a private/internal address. Ported the IP-pinning pattern already used by `explorer/routes/ontology.py`'s `_make_pinned_session` into the shared ingest guard: the one resolution that decides accept/reject is now also the one the connection is pinned to, via a custom `HTTPAdapter` that presents the real hostname over TLS SNI / Host header while connecting only to the validated IPs. Also closes the RFC 6598 Carrier-Grade NAT gap noted as a known limitation in #905/#868: `100.64.0.0/10` is now in `BLOCKED_NETWORKS`
+  - `ReportGenerator._generate_html()` (`export/report_generator.py`) f-string-interpolated report title/summary/metrics into HTML with no escaping — an ingested entity or document whose content flowed into a report (e.g. `<img src=x onerror=...>`) executed as stored XSS when the report was opened. All interpolated values are now `html.escape()`d
+  - `AnzoStore._format_object_for_sparql()` (`triplet_store/anzo_store.py`) validated the subject/predicate of a triplet via `sparql_escaping.validate_uri()` before interpolating them into a SPARQL `INSERT DATA` clause, but delegated the **object** position to a separate formatter that wrapped it as `<{obj}>` without the same validation — an object value containing `>`/`}`/`{`/`"` could close the intended `<...>` token early and inject additional SPARQL Update operations. The Blazegraph/RDF4J backends were hardened for the equivalent gap previously; Anzo's object position now goes through the same `validate_uri()` check
+  - Also hardened in the same pass: Apache AGE's `create_index()` `index_type` parameter is now allowlisted (was interpolated raw into a `USING` clause); Neo4j's `limit` is now explicitly validated (raises `ValidationError` for non-integer input instead of falling through to a generic `ProcessingError`); the `ffprobe` metadata-extraction subprocess call is guarded against a filename starting with `-` being parsed as an option; the MCP server no longer echoes raw exception text to JSON-RPC clients, logging full details server-side and returning a generic message plus the exception class name instead
+  - **Fixed during review** (@KaifAhmad1): the SSRF IP-pinning change introduced a connection-pool leak of its own — `requests.Session.mount()` silently drops whatever adapter it replaces without closing it, so a multi-hop redirect chain on a reused session leaked one pooled connection per hop. Pinned adapters are now tagged and explicitly closed before being replaced, both per-hop and on final restore
+  - **Fixed during review** (@KaifAhmad1): mounting a pinned adapter and setting a Host header on a caller-supplied `Session` is not inherently thread-safe — two guarded calls sharing the same session from different threads could interleave their mount/restore cycles. Added a per-session lock (`_get_session_lock`) so concurrent guarded calls on the same session now serialize instead of racing; verified with a two-thread test showing correct serialization and zero cross-contamination of per-request Host headers
+  - **Fixed during automated PR review** (Qodo): `export_table_data()`'s new identifier/fragment validation raised `ValidationError` from inside a `try` whose blanket `except Exception` re-wrapped it as `ProcessingError`, masking the distinction between "bad input" and "the export itself failed" that callers rely on elsewhere in this module. Added the `except ValidationError: raise` guard already used by its sibling methods
+  - **Fixed during automated PR review** (Qodo): on a hop where IP pinning doesn't apply (`allow_private_ips=True`), `_apply_connection_pin()` unconditionally popped the session's `Host` header instead of restoring whatever it was before pinning touched it — a caller-supplied session carrying its own legitimate `Host` override (e.g. fronting a private endpoint under a different name) had that override silently dropped for the in-flight request, only reappearing afterward via the outer `finally` restore. It now restores the session's own pre-call header state (set back if present, popped only if it was truly absent) instead of always popping
+  - **Fixed during automated PR review** (Qodo): the `where`/`order_by` blocklist matched keywords/punctuation inside properly quoted string literals and identifiers too, so legitimate data like `status = 'union'` or `name = 'a--b'` was rejected as if it were SQL syntax. The blocklist now runs against a copy with quoted-literal contents masked out (`_mask_sql_literals`) — a malformed/unterminated quote sequence doesn't match the masking pattern and is left fully exposed to the blocklist, so this closes false positives without opening a masking-based bypass; the fragment actually used in the query is unchanged
+  - Re-ran each finding's proof-of-concept (or an equivalent adversarial test) against the fix and confirmed it is blocked: tar path/symlink traversal (both lexical and resolved-path forms), SQL UNION exfiltration and identifier breakout, DNS-rebinding TOCTOU (including under a configured `HTTP_PROXY`, which the pinning adapter also rejects outright since a proxy would resolve DNS itself), stored XSS, and the AnzoStore SPARQL injection
+  - `pytest tests/ingest/`: 266 passed, 2 skipped (10 pre-existing failures unrelated to this change — identical failure set confirmed on unmodified `main`); full regression sweep across `graph_store`, `export`, `triplet_store`, `parse`, and backup/restore: 313 passed
+
+- **`Authorization`/`Proxy-Authorization` credentials could leak to a different origin across HTTP redirects, and several ingest paths bypassed the shared SSRF/redirect guard entirely** (#1067, closes #947) by @Sameer6305, reviewed by @KaifAhmad1
+  - `request_with_ssrf_guard()` previously only stripped sensitive headers from per-request `kwargs["headers"]` on a cross-origin redirect; session-level `Authorization`/`Proxy-Authorization` headers, `session.auth`, and `session.trust_env` (`.netrc` lookup) could all still resurrect credentials on the hop to a foreign origin. All five credential sources are now stripped case-insensitively, kept stripped for the remainder of a multi-hop redirect chain (no resurrection even if a later hop returns to the original host), and unconditionally restored via `finally` — including on exceptions and redirect-limit errors
+  - `MCPClient._send_request_http()` and `PublicAPIIngestor.detect_public_api()`/`ingest_public_api()` called `httpx.post()`/`requests.post()`/`session.request()` directly, bypassing `request_with_ssrf_guard()` entirely. Both now route through the shared guard, including when `validate_no_auth=False`
+  - `SeedDataManager.load_from_api()` mutated the caller-supplied `headers` dict in place when adding an API-key `Authorization` header, silently leaking the key back into a dict the caller might reuse elsewhere. Now copies before modifying
+  - **Fixed during review** (@KaifAhmad1): `allow_private_ips=True` (used to let MCP servers run on localhost/internal networks) was applied to every redirect hop, not just the operator-configured host — a compromised or malicious MCP server could 302-redirect to an internal address (e.g. `169.254.169.254` cloud metadata) and the guard would follow it unchecked, defeating the SSRF protection this PR otherwise adds. Added `allow_private_ips_on_redirect` to `request_with_ssrf_guard()`: a redirect target inherits the original host's private-IP trust only when it matches that host; any other host falls back to strict validation. `MCPClient` now pins `allow_private_ips_on_redirect=False`, so only same-host redirects on a trusted MCP server keep working — a cross-host hop into private address space is blocked
+  - **Fixed during review** (@KaifAhmad1): `detect_public_api()` only caught `requests.exceptions.RequestException`, but `request_with_ssrf_guard()` raises `ValidationError` (a disjoint hierarchy) for SSRF-blocked hosts, blocked redirect targets, missing `Location`, or exceeded redirect limits — unlike its sibling `ingest_public_api()`, which already caught it. Callers (including `is_public_api()`) got an undocumented raw `ValidationError` instead of `ProcessingError`, and the error-logging call was skipped. Now catches `(ValidationError, ProcessingError)` and re-raises, matching the sibling method
+  - **Fixed during review** (@KaifAhmad1): `detect_public_api()`/`ingest_public_api()` forwarded `**options` into `request_with_ssrf_guard(..., session=self.session, allow_private_ips=self.allow_private_ips, **request_options)` without stripping `session`/`allow_private_ips` from `request_options` first — a caller passing either through the per-call `**options` (a plausible mistake, since `allow_private_ips` is also a documented constructor-level knob) got a raw `TypeError: got multiple values for keyword argument`. Both are now popped from `request_options` before the call
+  - New regression coverage added during review: `TestAllowPrivateIpsOnRedirect` (cross-host redirect into private space blocked, same-host redirect trust preserved, default behavior unchanged for existing callers that don't pass the new kwarg) and `TestMCPClientAuthRedirect::test_redirect_to_private_ip_is_blocked`/`test_same_host_redirect_on_private_mcp_server_is_not_blocked` in `tests/ingest/test_auth_header_redirect_security.py`; `test_detect_public_api_propagates_ssrf_validation_error` and duplicate-kwarg regression tests for both methods in `tests/ingest/test_public_api_ingestor.py`
+  - `pytest tests/ingest/test_auth_header_redirect_security.py tests/ingest/test_public_api_ingestor.py tests/test_seed_manager.py tests/ingest/test_submodules.py tests/ingest/test_cookbook_integration.py`: 111 passed
+
+- **`FeedIngestor`/`FeedMonitor` (RSS/Atom feed ingestion) had no SSRF protection, allowing requests to internal/private network targets** (#928, closes #927) by @ZohaibHassan16
+  - `FeedIngestor.ingest_feed()`, `discover_feeds()` (link-tag fetch, common-path HEAD probe, and feed-validation GET), and `FeedMonitor.check_updates()` all called `requests.get()`/`requests.head()` directly with default redirect-following and no scheme allowlist or private/loopback/link-local IP validation — despite `semantica/ingest/ssrf.py`'s `request_with_ssrf_guard()` already existing and being used by `web_ingestor.py`/`api_ingestor.py`. `ingest_feed()`'s own URL check only verified `urlparse(url).scheme`/`.netloc` were non-empty, never that the scheme was http/https or that the resolved target IP was safe. Reachable via the public `ingest_feed()`/`ingest()` entry points with any caller-supplied feed URL
+  - All 5 call sites now route through `request_with_ssrf_guard()`, which validates scheme (http/https only) and resolved IP before the request, and re-validates every redirect `Location` before following it — closing both the direct-IP and redirect-chain SSRF paths. Added an `allow_private_ips` config option to both `FeedIngestor` and `FeedMonitor`, consistent with the other ingestors
+  - **Fixed during review** (Qodo): `test_discover_feeds_empty` mocked `requests.get`, which no longer executes now that the code path goes through `request_with_ssrf_guard()` (backed by `requests.request`) — the test was passing without exercising the real code. Corrected to mock `requests.request` and `socket.getaddrinfo`
+  - `pytest tests/ingest/test_feed_ingestor.py`: 12/12 passed. Independently reproduced the issue's own PoC (`FeedIngestor().ingest_feed("http://127.0.0.1:8765/feed.xml")` against a live local server) and confirmed it now raises `ValidationError` instead of succeeding
+  - **Known limitation carried over from `discover_feeds()`'s pre-existing design**: its common-path and feed-validation loops use a blanket `except Exception: continue`, which now also silently absorbs `ValidationError` from a blocked candidate URL the same way it already absorbed network failures — the request is still correctly blocked before reaching the network, so this is not an SSRF bypass, just a missed opportunity to log "blocked as SSRF target" distinctly from "unreachable"
+
+- **`RepoIngestor` clone surface hardened against GitPython URL/option injection** (#905, closes #868) by @pravit-amp
+  - `RepoIngestor.ingest_repository()` passed the caller-supplied repository URL and arbitrary `**options` straight through to `git.Repo.clone_from()` on a `GitPython>=3.1.50` floor predating hardening for `ext::`-style transport helpers and `$VAR`/`${VAR}` environment-variable expansion in clone URLs — unvalidated clone options (`upload_pack`, `multi_options`, `template`, `config`, `env`, ...) could be abused for command execution, and unvalidated hostnames allowed SSRF against internal services (e.g. cloud metadata endpoints)
+  - `GitPython` floor raised to `>=3.1.58`
+  - Clone options passed to `clone_from()` are now allowlisted to `{depth, branch, single_branch, no_tags}`; anything else raises `ValidationError` before the clone is attempted
+  - Repository URLs are validated before cloning: scheme allowlist (`https`, `http`, `git`, `ssh`), rejection of `$VAR`/`${VAR}` tokens, and hostname resolution with every returned address screened against private/loopback/link-local/unspecified ranges. scp-like SSH remotes (`user@host:path`) are recognized and normalized to `ssh://` before the clone call
+  - **Fixed during review** (@Sameer6305): the SSRF check originally used `ip.is_reserved`, which flags the NAT64 Well-Known Prefix (`64:ff9b::/96`, RFC 6052) as reserved — falsely blocking `github.com` and other public hosts on IPv6-only/dual-stack networks using NAT64. Narrowed the block list to private/loopback/link-local/unspecified only
+  - **Fixed during review** (@Sameer6305): local filesystem repository paths (`git clone /path/to/local/repo`) were being treated as remote URLs and rejected outright; local paths now bypass network validation entirely since they make no network requests and carry no SSRF risk
+  - **Known limitation**: the SSRF host check does not classify RFC 6598 Carrier-Grade NAT space (`100.64.0.0/10`) as blocked — Python's `ipaddress.IPv4Address.is_private` does not cover that range, so a hostname resolving into it (e.g. some Kubernetes/CNI pod networks) would not be caught. Follow-up recommended to add it explicitly alongside the existing private/loopback/link-local checks
+  - `pytest tests/ingest/test_repo_ingestor_security.py -v`: 44 passed
+
+- **HTTP response header injection via `node_id`, unbounded-memory DoS in link prediction, and unsanitized imported node IDs in the Explorer** (#912) by @Sunil56224972
+  - `semantica/explorer/routes/provenance.py`'s `GET /api/provenance/report` f-string-interpolated the `node_id` query parameter directly into the `Content-Disposition` response header; a `\r\n`-bearing `node_id` could inject arbitrary response headers (`Set-Cookie` session fixation, `Content-Type` override for reflected XSS). Fixed with `_safe_content_disposition_filename()`, which strips `\r`, `\n`, `\x00`, `"`, `\` and length-caps the value before interpolation
+  - `POST /api/enrich/links` (link prediction) loaded up to 999,999 nodes with no cap or concurrency guard, then scored every candidate — a single request could consume ~1.6 GB RAM, and concurrent requests compounded that with no limit. Capped the candidate pool at 10,000 nodes (`413` if exceeded) and added an `asyncio.Semaphore(2)`, mirroring the SPARQL DoS fix in #898
+  - `POST /api/import` stored uploaded JSON/CSV node IDs verbatim; since provenance reports reflect `node_id` into `Content-Disposition`, an attacker could upload a node with a CRLF-bearing ID once and trigger the header-injection chain above for every subsequent viewer. Added `_sanitize_import_node_id()`, applied to node and edge `source_id`/`target_id` fields on both the JSON and CSV import paths
+  - **Corrected during review**: the JSON import path had a second, unsanitized branch — any uploaded node object already carrying a `"properties"` key (the shape this app's own `/api/export` produces, and already used elsewhere in the test suite) was appended to the graph as-is, bypassing `_sanitize_import_node_id()` entirely and leaving the stored-header-injection chain open via a one-line payload (`{"id": "<crlf>", "properties": {}}`). That branch now sanitizes `id` before storing
+  - **Corrected during review**: the link-prediction cap checked `total` only *after* calling `session.get_nodes()`/`get_edges()`, which normalize the graph's *entire* matching node/edge set before applying `limit` — so the guard ran after the expensive work it was meant to prevent had already happened, on every request regardless of graph size. Added `GraphSession.get_raw_counts()`, an O(1) check against the raw `len(graph.nodes)`/`len(graph.edges)` collections, and moved the size check ahead of the normalizing calls
+  - **Corrected during review**: 5 of the original PR's 22 regression tests asserted that literal words like `"Set-Cookie"`/`"Content-Type"` disappeared from the sanitized value — the sanitizer only strips `\r\n\x00"\\`, not letters, so those assertions failed against the PR's own fix as submitted. Corrected to assert on the property that actually blocks header injection (no `\r`/`\n` survives), and added end-to-end tests that exercise the real `/api/import` → `/api/provenance/report` route chain (not just the standalone sanitizer function) so the `properties`-key bypass has regression coverage
+  - Full `explorer` suite: 241 passed; `tests/test_security_regression_pr2.py`: 30 passed
+
+- **`fastapi`/`python-multipart` floors in the `explorer` extra allowed PYSEC-2024-38 (CVE-2024-24762 / GHSA-2jv5-9r88-3w3p, `python-multipart` ReDoS)** (#871, closes #869) by @agu2347
+  - `explorer` declared `fastapi>=0.100.0` and `python-multipart>=0.0.6`; both floors resolve to versions carrying a ReDoS in `python-multipart`'s `Content-Type` header option parser (`parse_options_header`), reachable by any endpoint that accepts form/multipart data — an attacker-crafted header option can stall the event loop for minutes
+  - **Corrected during review**: the original fix raised only `fastapi>=0.109.1`, leaving `python-multipart>=0.0.6` unchanged. `python-multipart` is declared as its own direct dependency in the `explorer` extra rather than pulled in transitively via `fastapi[all]`, so a bare `fastapi` install enforces no `python-multipart` floor at all — the vulnerable `0.0.6` could still resolve with `fastapi>=0.109.1` in place. Floors raised to `fastapi>=0.109.2` / `python-multipart>=0.0.7`, the first versions of each that exclude the vulnerable range
+  - **Fixed along the way**: the `Security` workflow's `pip-audit` job ran only on a weekly schedule with `continue-on-error: true`, against a bare Python environment with none of Semantica's optional extras installed — it would never have seen `fastapi`/`python-multipart` regardless of which floor was pinned. `security-scan.yml`'s Safety check has the same blind spot (`pip install -e ".[llm-litellm]"` only, never `[explorer]`). `pip-audit` now also runs on `pull_request` when `pyproject.toml` changes, installs `semantica[all]`, and fails the build on any finding for that trigger; the schedule/`workflow_dispatch` runs stay non-blocking pending a full pass over any pre-existing findings across the whole `[all]` tree
+  - **Caught by the new gate on its first run**: `python -m pip install -e ".[all]"` pulled in `setuptools==79.0.1`, vulnerable to CVE-2026-59890/GHSA-h35f-9h28-mq5c/PYSEC-2026-3447 (Unicode-normalization bypass of `MANIFEST.in` exclude/prune patterns on macOS APFS/HFS+, letting excluded files leak into a built sdist), fixed in `83.0.0`. `[build-system] requires` had the exact same too-permissive-floor pattern this whole entry is about (`setuptools>=61.0`), and `actions/setup-python`'s baked-in `setuptools` isn't governed by that pin at all since it's outside any isolated build. Bumped `[build-system] requires` to `setuptools>=83.0.0`, and the `Security` workflow now runs `pip install --upgrade pip setuptools` before auditing so the scanned environment can't have a stale ambient copy regardless of what governs it
+  - Full `explorer` suite: 241 passed
+
+- **`SeedDataManager.load_from_api()` made unguarded HTTP requests, with no SSRF protection at all** (#942) by @ZohaibHassan16
+  - `load_from_api()` called `requests.get()` directly instead of going through `semantica/ingest/ssrf.py`'s `request_with_ssrf_guard()`, unlike every other ingestor in this module — a caller-supplied `api_url` could target internal/private network addresses with no validation. Now routes through the shared guard, gaining redirect validation and bounded DNS resolution for free
+  - **Follow-up** (#959, closes #943) by @yunaremaia: added an `allow_private_ips` opt-in (parsed via the shared `parse_bool` helper) for trusted internal deployments that legitimately need to load from a private-network API, while keeping the guard's block-by-default behavior for everyone else
+
+## [0.6.5] - 2026-08-11
+
 ### Added
 
 - **Embedded Oxigraph backend for `TripletStore`** (#838, closes #834) by @Linxiushen
@@ -67,8 +515,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Entities and relationships round-trip as memory-local provenance only — Markdown import intentionally does not write into `ContextGraph`, matching the MVP scope agreed on in #765
   - Documented the file contract and workflow in `docs/reference/context.md`; 43 new tests in `tests/context/test_agent_memory_markdown.py` cover round-trip losslessness, idempotency, validation errors, rollback on failure, and vector-store sync ordering
 
+- **Markdown directory round trips for `ContextGraph`** (#852) by @SaurabhScripts
+  - `ContextGraph.save_to_file(..., format="markdown")` and `load_from_file(..., format="markdown")` persist a deterministic `graph.md` relationship manifest plus one human-editable Markdown file per node, preserving graph, node, edge, family, temporal, and cross-graph link identities
+  - Imports validate the complete directory before replacing graph state, rebuild indexes and analytics state atomically, create JSON-compatible stub nodes for dangling edge endpoints, and emit the same granular node/edge audit events as JSON loading
+  - Existing exports are replaced atomically only after their complete canonical layout is validated; untracked files, renamed node files, symlinks, Windows directory junctions, and other reparse points cause a fail-closed error instead of authorizing directory deletion
+  - Added 30 focused tests covering deterministic round trips, manual edits, validation rollback, managed-directory identity, publish rollback, audit-manager compatibility, stale-cache clearing, mocked and real Windows junctions, and missing-path behavior
+
 ### Fixed
 
+- **Markdown import followed filesystem links even though Markdown export already refused to overwrite them** (#851, follow-up to #765, #786) by @SaurabhScripts
+  - `AgentMemory._read_markdown_path()` now rejects symlink files, broken symlinks, symlinked directories, Windows directory junctions, and other Windows reparse points supplied directly; linked entries discovered inside an otherwise valid directory are safely skipped, preserving the current directory-import contract
+  - `_read_markdown_file_content()` re-checks the file and parent directory immediately before and after opening, uses `O_NOFOLLOW` where available, and verifies the resulting descriptor is a regular file via `fstat`/`S_ISREG`, so link swaps are rejected rather than silently followed
+  - Junction detection uses `os.path.isjunction()` where available and falls back to the Windows reparse-point file attribute on older Python versions; export applies the same link check before replacing a Markdown file
+  - Documented the import restriction in `docs/reference/context.md`; added 11 tests to `tests/context/test_agent_memory_markdown.py` covering file/directory/broken-symlink rejection, simulated open races, mocked and real Windows junctions, and the reparse-point fallback
+  - Any additional review follow-up commits land in this same PR/entry rather than as a separate changelog item
+
+- **`PipelineWithProvenance` raised `ModuleNotFoundError` on import and `AttributeError` on `.run()`** (#858, closes #858) by @Karunasagar12
+  - `from .pipeline import Pipeline` failed because `semantica/pipeline/pipeline.py` does not exist; corrected to `from .pipeline_builder import Pipeline`
+  - `.run()` called `self._pipeline.run()` on the `Pipeline` dataclass, which has no such method; replaced with `self._engine.execute_pipeline(self._pipeline, ...)` delegating to `ExecutionEngine`
+  - Constructor now accepts a built `Pipeline` instance (from `PipelineBuilder.build()`) instead of `**config`; the old `Pipeline(**config)` internal construction was invalid and never functional
+  - Replaced deprecated `datetime.utcnow()` with `datetime.now(timezone.utc)` in `run()`
+
 - **`VectorStore.search_vectors()` returned inconsistent result shapes across backend implementations** (#853, closes #845) by @Sameer6305, reviewed by @KaifAhmad1
   - Every built-in backend (FAISS, Milvus, pgvector, Pinecone, Qdrant, SQLite-vec, Weaviate, in-memory) now returns the same canonical `SearchResult` shape (`id`, `score`, `metadata`, `vector`, `distance`), instead of some backends omitting `vector`/`metadata`/`distance` or, for Weaviate, returning a backend-specific `properties` key instead of `metadata`
   - Added a `SearchResult` `TypedDict` (`semantica/vector_store/vector_store.py`, exported from `semantica.vector_store`) documenting the contract; `metadata` now always defaults to `{}` rather than being absent, and `id` accepts `Union[str, int]` to accommodate Milvus/Qdrant's native integer IDs without casting
@@ -244,6 +711,57 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Security
 
+- **DNS check-then-use hardening for the ontology URL fetcher, and a remaining object-IRI validation gap** (#916, follow-up to GHSA-8c7v-62gr-hj6g and GHSA-8vgg-8mr4-r236) by @KaifAhmad1
+  - **DNS check-then-use (TOCTOU) window**: GHSA-8c7v-62gr-hj6g's own fix description flagged this as a secondary gap — `_validate_fetch_url()` resolved and validated a hostname once, but `_fetch_url_sync()` then let `requests` resolve the same hostname again independently at connect time. A low-TTL or rebinding DNS answer could differ between the two lookups, reopening the SSRF window the validation exists to close
+  - `_validate_fetch_url()` now returns the validated IP, and a new `_make_pinned_session()` builds a per-hop `requests.Session` whose connection pool is pinned directly to that IP — bypassing DNS resolution for the connection entirely — while explicitly restoring the real hostname as the outgoing HTTP `Host` header and, for HTTPS, the TLS SNI `server_hostname`/`assert_hostname`, so the connection reaches the validated IP but still presents (and is verified against) the real hostname's identity, keeping virtual hosting and certificate validation correct
+  - Caught during implementation: an earlier draft set urllib3's `_dns_host` post-construction, assuming (as in some urllib3 releases) that it was decoupled from `host`. In the version this project installs (2.7.0), `host` is a property that reads/writes `_dns_host` directly, so that approach would have silently changed the Host header too — caught by an end-to-end test against a real local server before landing, rather than shipping. Verified with real (non-mocked) local HTTP and HTTPS servers, the latter using a generated self-signed certificate to prove SNI/cert-hostname verification checks the real hostname rather than the pinned IP, plus a negative control confirming a hostname/cert mismatch is still correctly rejected, not silently bypassed
+  - **Object-IRI validation gap** (GHSA-8vgg-8mr4-r236 follow-up, distinct from the object-branch fix already shipped in #911): a triplet object already wrapped in `<...>` skipped `sparql_escaping.validate_uri()` in both `blazegraph_store.py` and `rdf4j_store.py`'s `_format_object_for_sparql`/`_format_object_for_ntriples`, only checking the inner content for a literal space or `>` — the pre-wrapped and unwrapped branches now validate identically
+  - **Fixed along the way** (caught in automated review across two follow-up rounds): `_validate_fetch_url()` originally pinned to only the first resolved IP, so a hostname with multiple A/AAAA records would fail outright if that specific address was unreachable — it now returns every validated IP and `_make_pinned_session()` falls back through all of them, verified by pinning to a genuinely unreachable address followed by a working one and confirming the fetch still succeeds; the test HTTPS server allowed TLSv1/TLSv1.1 by not setting a minimum version, now pinned to TLSv1.2; and when an HTTP(S) proxy applied, pinning was silently skipped in favor of the unpinned path — proxies are now disabled outright for this fetcher (`session.trust_env = False`, so `HTTP_PROXY`/`HTTPS_PROXY` env vars are never consulted) with a fail-closed 502 backstop if a proxy is ever forced onto the session some other way, verified by pointing `HTTP_PROXY` at an address that would fail if actually used and confirming the fetch still succeeds directly
+  - New `tests/explorer/test_ontology_dns_pinning.py` (12 tests: real local HTTP/HTTPS servers including 2 real-TLS checks, multi-IP fallback success/failure, and no-proxy-trust verification — gracefully skipped without the optional `cryptography` package where applicable); updated `tests/explorer/test_ontology_ssrf.py` for the new per-hop session construction; 4 new tests in `tests/triplet_store/test_sparql_injection.py` for the object-IRI fix. Full `explorer` + `triplet_store` suite: 572 passed
+
+- **Missing Origin validation on the `/ws/graph-updates` WebSocket handshake** (#917, GHSA-4643-wpgq-w329) by @KaifAhmad1
+  - `CORSMiddleware` doesn't cover WebSocket handshakes at all (Starlette's CORS support only wraps HTTP), so under `SEMANTICA_ALLOW_ANONYMOUS=true` — the mode `docker-compose.dev.yml` ships — the anonymous-mode key bypass accepted a `/ws/graph-updates` connection from any origin. Loopback binding isn't a boundary against a browser: any page the operator has open can still reach `ws://localhost:8000/ws/graph-updates` directly, and `ConnectionManager.broadcast` sends every `graph_mutation` to every connected socket with no per-connection scoping. Combined with `/api/import` accepting `multipart/form-data` (a CORS-safelisted content type that skips preflight), a hostile page could write to the graph over REST and read the result back over the unauthenticated WebSocket
+  - Not affected: any deployment with `SEMANTICA_API_KEY` configured — the handshake already rejects without a valid key in that mode. This was an anonymous-mode-only, development-configuration exposure
+  - Fix: check the handshake's `Origin` header against `app.state.explorer_settings['allowed_origins']` — the same list `CORSMiddleware` already enforces for HTTP — before the key check. A missing `Origin` (native/CLI clients, which never set the header) is still allowed through, since the browser is the only threat this closes
+  - 4 new tests in `tests/explorer/test_explorer_auth.py`: hostile Origin rejected under anonymous mode; hostile Origin rejected even with a correct key (Origin is checked first, so a leaked key alone can't hijack the socket); an allowlisted Origin still connects; a missing Origin still connects. Full `explorer` suite: 226 passed
+
+- **Polynomial-time ReDoS in the SPARQL route's `_PREFIX_DECL` regex** (#915, CodeQL `py/polynomial-redos`) by @Sameer6305
+  - The prior pattern's trailing `\s*` overlapped with the preceding `<[^>]*>` IRI-body match on inputs containing no closing `>` (e.g. `base<` followed by thousands of `!<` repetitions), forcing the regex engine to explore every possible split between the two quantifiers — O(n²) backtracking reachable from `req.query` via `_is_read_only_query()`
+  - Fixed by making the two quantifiers character-disjoint: horizontal whitespace only (`[ \t]`, never overlapping the IRI body) instead of `\s*`, and excluding CR/LF from the IRI body (`[^>\r\n]*`) so it can never span a line boundary. Independently verified: the exact pathological payload (`base<` + `!<` × 5,000/20,000) scales linearly (0.238ms → 0.841ms for 4x input, not the ~16x a surviving quadratic blowup would show)
+  - Added `_SPARQL_MAX_QUERY_LEN = 10_000` as defense-in-depth, checked in `execute_sparql()` before any regex work so a future pattern regression stays bounded regardless
+  - Two correctness regressions raised in review were checked and did not reproduce: comment-then-prefix stripping order means an inline comment after a `PREFIX` line (`PREFIX ex: <...> # comment`) is already gone by the time `_PREFIX_DECL` runs, verified directly against the pipeline; and the allowlist's `.sub()`-based cleaning only ever affects the yes/no decision, never the query actually sent to `graph.query()` — so even the narrow case of a multi-line string literal that happens to start a line with the literal text `PREFIX` or `BASE` can only cause a legitimate query to be wrongly rejected, never let something malicious through, since rdflib's parser still gates whatever actually executes
+  - 20 new/updated tests in `tests/explorer/test_sparql_route.py` and `tests/test_security_regression.py` (inline prologues, CRLF line endings, multi-line CRLF prefix chains, oversized-query rejection). 225 `explorer` + 82 SPARQL-specific tests passing
+
+- **SPARQL injection via unvalidated triplet IRIs** (#911, GHSA-8vgg-8mr4-r236) by @KaifAhmad1
+  - `Triplet.subject`/`.predicate` (and, in some builders, `.object`) were interpolated directly into SPARQL update/query strings in the Blazegraph and RDF4J stores, and into a SELECT filter in the Jena store. A subject containing `>` closes the `<...>` IRI token early, so the rest of the value is parsed as more SPARQL. Entity names are document text in the normal ingest pipeline, so anyone whose content gets processed could append operations like `CLEAR ALL`, running with the application's store credentials
+  - Applied the existing `sparql_escaping.validate_uri` (already used by `anzo_store.py`, the one backend that was already hardened — this generalizes its approach rather than inventing a new one) at every subject/predicate/object interpolation site: `blazegraph_store.py`'s `_build_insert_data`, `_triplets_to_rdf`, `bulk_load`'s `graph` option, `get_triplets`'s filter, and `delete_triplet`; `rdf4j_store.py`'s `_triplets_to_ntriples`, `get_triplets`'s filter, and `delete_triplet`; `jena_store.py`'s `get_triplets`'s filter (the only vulnerable site there — `add_triplets`/`delete_triplet` already use rdflib's native `Graph.add`/`.remove` with `URIRef` rather than building query strings)
+  - **Fixed along the way** (caught in review, by @ZohaibHassan16): `_format_object_for_sparql`'s URI branch — used when a triplet's *object* is itself a URI rather than a literal — only checked for spaces and `>` inline instead of running the same `validate_uri` check applied to subject/predicate, leaving the object position as a narrower but real gap in both Blazegraph and RDF4J. Also fixed test flakiness in `RDF4JStore`'s test fixtures, which weren't mocking `_connect()` and so were making real network calls
+  - New `tests/triplet_store/test_sparql_injection.py` (12+ tests) reproducing the advisory's own injection payload (`http://example.com/a> ... ; CLEAR ALL ; INSERT DATA { ...`) against all three backends' write and read paths, asserting the malicious query is never built or sent. Full triplet_store suite: 330+ tests passing
+  - Side note, not part of this fix: found that `jena_store.py`'s `get_triplets()` builds syntactically invalid SPARQL for its WHERE-clause filters (missing a `FILTER()`/separator before the equality conditions) — a pre-existing correctness bug, unrelated to the injection fix, left alone here and worth a separate follow-up
+
+- **Cypher injection via unvalidated node labels, relationship types, and property keys** (#910, GHSA-482h-hw99-h62p) by @KaifAhmad1
+  - Node labels and property keys passed to `create_node`/`create_relationship` were interpolated directly into Cypher strings in the Neptune, Neo4j, and FalkorDB graph stores. Property *values* are parameterized, but labels and keys can't be bound as query parameters, and nothing validated them — so a document-derived entity type or property name (the normal ingest path) could close the current Cypher token early and append arbitrary statements (e.g. `DETACH DELETE`), running with the application's database credentials
+  - New shared `semantica/graph_store/query_sanitize.py`: `sanitize_identifier()` generalizes `age_store.py`'s existing `_sanitize_label`/`_sanitize_rel_type` (the only backend that already validated this) into a helper the other backends import without an import cycle with `graph_store.py`/`methods.py`
+  - Applied at every label/relationship-type/property-key interpolation site in `amazon_neptune.py`, `neo4j_store.py`, `falkordb_store.py`, `graph_store.py` (`degree_centrality`'s own query builder), and `methods.py` (`update_relationship`'s own query builder) — covers `create_node`, `create_nodes`, `create_relationship`, `get_nodes`, `get_relationships`, `get_neighbors`, `shortest_path`, `update_node`, `create_index`, and all relationship-type filters across the three backends
+  - **Fixed along the way** (caught in review, by @Sameer6305): `depth`/`max_depth` path-length parameters are meant to be integers, but `Neo4jStore.get_neighbors()`/`shortest_path()` interpolated them into the Cypher variable-length-path syntax (`*1..{depth}`) without coercion — unlike the Neptune/FalkorDB equivalents, which already cast to `int()`. A string `depth` (e.g. `"1]->(x) DETACH DELETE x //"`) reached the query verbatim. Added the same `int()` coercion Neptune/FalkorDB already had, plus `GraphStore.get_neighbors()`'s `hops`/`depth` alias resolution
+  - New `tests/graph_store/test_cypher_injection.py` (unit tests on `sanitize_identifier` plus the labels/keys/rel-types injection payload run against Neptune/Neo4j/FalkorDB `create_node`/`create_relationship`, asserting the malicious query is never built or sent) and the depth-coercion regression above; plus additions to `tests/test_graph_store.py` (`degree_centrality`) and `tests/test_graph_store_methods.py` (`update_relationship`). Full graph_store suite: 224+ tests passing
+
+- **4 critical/high vulnerabilities in the Explorer API and vector store: RCE, SSRF, XXE, and DoS, plus Cypher/SPARQL injection hardening found along the way** (#898) by @Sunil56224972
+  - **[CWE-502] Arbitrary code execution via `pickle.load()`**: `VectorStore.save()`/`load()` used `pickle` for the on-disk `store_data.pkl`; a crafted `.pkl` file placed in the store directory (file upload, shared filesystem, or supply-chain compromise) could execute arbitrary code on deserialization. Replaced with JSON — vectors and metadata are fully JSON-serializable, so nothing is lost — and `load()` now refuses any legacy `.pkl` file it finds with a migration error rather than deserializing it
+  - **[CWE-918] SSRF via redirect bypass in `ontology.py`'s URL fetcher**: `_validate_fetch_url()` correctly blocked private/loopback/reserved addresses on the caller-supplied URL, but `_fetch_url_sync()` fetched with `allow_redirects=True`, so a validated *public* first hop could 302 to `http://169.254.169.254/...` (cloud instance metadata) or an internal service, and `requests` followed it with no re-check. Redirects are now followed manually, capped at 5 hops, with `_validate_fetch_url()` re-run against every hop's target — including relative `Location` headers, resolved via `urljoin()` before validation — and every response (redirect or final) is explicitly closed to avoid leaking connections back to the pool
+  - **[CWE-611] XXE injection in the RDF/XML parser**: `_safe_parse_rdf()` depended on `defusedxml` for XXE protection, but `defusedxml` wasn't declared in `pyproject.toml`'s `explorer` extra, so it was silently absent in normal installs and the code fell back to a bare warning plus unsafe parsing — a crafted RDF/XML ontology with an external entity could read arbitrary server files. Added `defusedxml>=0.7.1` to the extra, and `_safe_parse_rdf()` now fails closed: it raises rather than parsing untrusted RDF/XML if `defusedxml` isn't importable, replacing an earlier regex-based DOCTYPE-stripping fallback that was reviewed and rejected as bypassable
+  - **[CWE-770] DoS via unbounded SPARQL graph materialization**: `_build_rdflib_graph()` loaded up to 999,999 nodes and 999,999 edges into memory per query, and with up to 4 concurrent SPARQL requests permitted, an attacker could exhaust server memory. Added a 50,000 node/edge cap (`_SPARQL_MAX_GRAPH_NODES`); oversized graphs now return a clean error instead of attempting materialization
+  - **Cypher injection via Apache AGE's `graph_name` and `$$`-delimiter breakout**: `graph_name` was interpolated unvalidated into `cypher('{graph_name}', $$ ... $$)`, and raw Cypher query text containing `$$` could close AGE's dollar-quoted string delimiter early and append arbitrary SQL. `graph_name` is now validated against the same identifier allowlist `age_store.py` already used for labels/relationship types, and any query containing `$$` is rejected outright
+  - **SPARQL Explorer route (`/api/sparql`) hardened against comment/PREFIX-hiding bypass**: `_is_read_only_query()` now strips comments and PREFIX/BASE declarations before checking the leading keyword, and additionally scans the full query body for SPARQL Update keywords (INSERT/DELETE/DROP/LOAD/CLEAR/CREATE/COPY/MOVE/ADD) — so `SELECT ... ; DROP ALL` is now rejected by the keyword scan itself rather than relying solely on rdflib's parser
+  - **Fixed along the way** (maintainer follow-up, addressing automated review findings and a regression introduced across several rounds of iteration on the original fix):
+    - `VectorStore.save()`'s numpy handling used `list(v)` for the JSON fallback path, which produces `numpy.float32` elements that `json.dump()` can't serialize — changed to `v.tolist()`
+    - the SPARQL graph-size `ValueError` was raised outside `execute_sparql()`'s exception handling and surfaced as an unhandled 500 instead of a clean API error — moved inside
+    - every streamed `requests` response in the ontology redirect loop, including the one actually read and returned, is now closed in a `finally` block — a connection-pool leak that a rework of the redirect logic had briefly reintroduced after an earlier fix
+    - a later commit meant to add opt-in API-key auth (`explorer/auth.py`, gated on `EXPLORER_API_KEY`) instead **replaced and silently disabled** the `Depends(require_auth)` enforcement already merged into `main` for GHSA-j4mq-hprp-987v (Critical — unauthenticated Explorer API), removed the `/ws/graph-updates` handshake check, and — unlike `require_auth` — failed *open* (allowed all requests) whenever its key was unset. Merging that version would have silently reverted an already-fixed Critical CVE the moment this branch landed. Removed `explorer/auth.py`; restored the per-router `Depends(require_auth)` wiring and the WebSocket auth check; kept the one genuine improvement in that commit (adding `X-API-Key` to the CORS `allow_headers` list) by folding it into the existing CORS config
+    - the new SPARQL keyword-scan's comment-stripping regex (`#[^\n]*`) also matched the `#` inside standard RDF namespace IRIs (e.g. `.../1999/02/22-rdf-syntax-ns#`), corrupting any query with a normal `rdf:`/`rdfs:`-style `PREFIX` declaration — caught because the hardening's own bundled tests failed against two of its own cases. Fixed by only treating `#` as a comment-start at line-start or after whitespace; the companion `PREFIX`/`BASE` regex was also fixed to accept bare `BASE <...>` declarations, which have no prefix-name token between the keyword and the IRI
+  - New/updated regression tests: `tests/explorer/test_ontology_ssrf.py` (redirect re-validation, relative-redirect resolution, response closing, redirect-cap enforcement), `tests/test_security_regression.py` (Cypher/SPARQL injection, XXE, numpy serialization, SSRF redirect handling), plus additions to `tests/explorer/test_sparql_route.py`, `tests/vector_store/test_vector_store.py`, and `tests/explorer/test_explorer_auth.py`
+  - Note: the Cypher-injection hardening here is scoped to `age_store.py`'s `graph_name`/`$$` breakout, found while reviewing this PR. The broader label/property-key/relationship-type injection across the Neptune, Neo4j, and FalkorDB backends (GHSA-482h-hw99-h62p, #910) and the triplet-store SPARQL injection across Blazegraph/RDF4J/Jena (GHSA-8vgg-8mr4-r236, #911) are covered by separate, still-open PRs, as is the unauthenticated-Explorer-API fix referenced above (GHSA-j4mq-hprp-987v, #909, already merged)
+
 - **CI/CD supply-chain hardening against mutable-tag Action compromise (LiteLLM/Trivy-class attack)** (#824) by @KaifAhmad1
   - Every third-party GitHub Action across all 8 workflows is now pinned to a full commit SHA instead of a mutable tag (`@v7` → `@3d3c42e... # v7`), closing the exact vector used against LiteLLM in March 2026 (a compromised Trivy Action tag stole a long-lived publishing token)
   - Added `verify-action-pins.yml` + `.github/scripts/verify-action-pins.sh`: a CI check that fails closed on any `uses:` reference that isn't a full SHA (catching a newly introduced mutable tag, not just auditing existing pins) and re-verifies every pin against the GitHub API on each workflow change, on push to `main`, and weekly; an unresolvable API lookup is treated as a failure rather than a silent skip
@@ -1128,4 +1646,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ---
 
-For detailed release notes, see [GitHub Releases](https://github.com/Hawksight-AI/semantica/releases).
+For detailed release notes, see [GitHub Releases](https://github.com/semantica-agi/semantica/releases).

CODE_OF_CONDUCT.md

@@ -58,7 +58,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement through
-[GitHub Issues](https://github.com/Hawksight-AI/semantica/issues) with "[CoC]" prefix.
+[GitHub Issues](https://github.com/semantica-agi/semantica/issues) with "[CoC]" prefix.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

CONTRIBUTING.md

@@ -2,20 +2,20 @@
 
 Thank you for your interest in contributing! Every contribution, no matter how small, is valuable. 🎉
 
-⭐ **Give us a Star** • 🍴 **[Fork Semantica](https://github.com/Hawksight-AI/semantica/fork)** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**
+⭐ **Give us a Star** • 🍴 **[Fork Semantica](https://github.com/semantica-agi/semantica/fork)** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**
 
-> **New to contributing?** Start with a [`good first issue`](https://github.com/Hawksight-AI/semantica/labels/good%20first%20issue) or join our [Discord](https://discord.gg/sV34vps5hH) community.
+> **New to contributing?** Start with a [`good first issue`](https://github.com/semantica-agi/semantica/labels/good%20first%20issue) or join our [Discord](https://discord.gg/sV34vps5hH) community.
 
 ---
 
 ## 🚀 Quick Start
 
-1. Find a [`good first issue`](https://github.com/Hawksight-AI/semantica/labels/good%20first%20issue)
-2. [Fork Semantica](https://github.com/Hawksight-AI/semantica/fork) & clone the repository
+1. Find a [`good first issue`](https://github.com/semantica-agi/semantica/labels/good%20first%20issue)
+2. [Fork Semantica](https://github.com/semantica-agi/semantica/fork) & clone the repository
 3. Make your changes
 4. Submit a pull request!
 
-**Need help?** Join [Discord](https://discord.gg/sV34vps5hH) or [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions)
+**Need help?** Join [Discord](https://discord.gg/sV34vps5hH) or [GitHub Discussions](https://github.com/semantica-agi/semantica/discussions)
 
 ---
 
@@ -25,9 +25,9 @@ If you want to work on an open GitHub issue, please follow these steps to keep t
 
 1. **Check the issue.** Look at the issue's assignees and recent comments. If someone is already actively working on it, consider a different issue or ask in the comments whether help is welcome.
 
-2. **Comment before you start.** Leave a comment on the issue saying you'd like to work on it — something like *"I'd like to take this on"* is enough. This gives maintainers the context they need to assign the issue appropriately.
+2. **Comment if you'd like the issue reserved.** Leaving a comment like *"I'd like to take this on"* is the fastest way to get assigned, but it isn't required — maintainers can also assign an issue directly to a contributor (e.g., based on recent activity in the repo) without waiting for a comment first.
 
-3. **Wait for assignment.** A maintainer will review the request and assign the issue when appropriate. Please wait for this before investing significant time in implementation, as priorities and approaches can shift.
+3. **Wait for assignment.** A maintainer will assign the issue when appropriate, whether or not a comment was left. Please wait for this before investing significant time in implementation, as priorities and approaches can shift.
 
 4. **Create a branch and implement.** Once assigned, fork the repository (if you haven't already), create a dedicated branch, and begin your work.
 
@@ -37,9 +37,23 @@ If you want to work on an open GitHub issue, please follow these steps to keep t
 
 5. **Open a focused PR and link the issue.** When you're ready, open a pull request and reference the issue in the description (e.g., `Closes #123`). Keep the PR scoped to the work described in the issue.
 
-> **Why this matters:** Commenting before opening a PR helps maintainers track who is working on what, assign issues correctly, and prevent two contributors from solving the same problem independently. It also gives you a chance to align on the expected approach before writing code.
+> **Why this matters:** Assignment (with or without a comment) helps maintainers track who is working on what and prevent two contributors from solving the same problem independently. It also gives you a chance to align on the expected approach before writing code.
 
-Not sure where to start? Try a [`good first issue`](https://github.com/Hawksight-AI/semantica/labels/good%20first%20issue) or ask in [Discord](https://discord.gg/sV34vps5hH).
+Not sure where to start? Try a [`good first issue`](https://github.com/semantica-agi/semantica/labels/good%20first%20issue) or ask in [Discord](https://discord.gg/sV34vps5hH).
+
+---
+
+## 🔀 Duplicate PRs & Issue Priority
+
+When more than one pull request targets the same issue, maintainers triage using this order of priority. These rules decide between PRs that are otherwise following the [assignment workflow above](#-working-on-an-existing-issue) — opening a PR before being assigned doesn't grant priority on its own, and an unassigned PR can still be closed as a duplicate once someone else is assigned to the issue.
+
+1. **Contributor-raised issue with an existing PR.** If the person who opened the issue has also opened a PR for it, that PR is prioritized (they still need to be assigned before it's merged).
+2. **Maintainer-raised issue with a claim comment.** If we opened the issue and someone has commented asking to work on it, we assign it to them and check their PR before picking up any other PR for the same issue.
+3. **No prior assignment or comment.** If multiple PRs exist and no one was assigned or claimed the issue first, priority goes to whichever contributor has the most consistent activity in the repo over the last 60 days (e.g., merged PRs, substantive reviews, or issue triage participation) — not just PR volume.
+4. **Late duplicate PRs.** If a PR is opened after another contributor has already been assigned to the issue, we close the duplicate early rather than let it sit open, and point the author to another open issue (or ask them to check `main` for newly opened ones). This avoids contributors spending time updating a PR that won't be merged.
+5. **Overlapping scope.** If a PR covers multiple issues, or there's genuine overlap between competing PRs, maintainers discuss it on [Discord](https://discord.gg/sV34vps5hH) before deciding rather than resolving it unilaterally.
+
+**Why this matters:** it keeps triage predictable, avoids wasted contributor effort on PRs that won't merge, and helps retain active contributors.
 
 ---
 
@@ -102,7 +116,7 @@ Not sure where to start? Try a [`good first issue`](https://github.com/Hawksight
 
 **What:** Report bugs you find
 
-**How:** Use the [bug report template](https://github.com/Hawksight-AI/semantica/issues/new?template=bug_report.md)
+**How:** Use the [bug report template](https://github.com/semantica-agi/semantica/issues/new?template=bug_report.md)
 
 **Include:** Description, steps to reproduce, expected vs actual behavior, environment details
 
@@ -112,7 +126,7 @@ Not sure where to start? Try a [`good first issue`](https://github.com/Hawksight
 
 **What:** Suggest new features or improvements
 
-**How:** Use the [feature request template](https://github.com/Hawksight-AI/semantica/issues/new?template=feature_request.md)
+**How:** Use the [feature request template](https://github.com/semantica-agi/semantica/issues/new?template=feature_request.md)
 
 **Include:** Problem statement, proposed solution, use cases
 
@@ -132,7 +146,7 @@ Not sure where to start? Try a [`good first issue`](https://github.com/Hawksight
 
 **What:** Help others in the community
 
-**Where:** [Discord](https://discord.gg/sV34vps5hH), [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions)
+**Where:** [Discord](https://discord.gg/sV34vps5hH), [GitHub Discussions](https://github.com/semantica-agi/semantica/discussions)
 
 **Examples:** Answer questions, review PRs, share your projects
 
@@ -159,12 +173,12 @@ Not sure where to start? Try a [`good first issue`](https://github.com/Hawksight
 
 ### 1. Fork & Clone
 
-First, [fork Semantica](https://github.com/Hawksight-AI/semantica/fork) on GitHub, then:
+First, [fork Semantica](https://github.com/semantica-agi/semantica/fork) on GitHub, then:
 
 ```bash
 git clone https://github.com/your-username/semantica.git
 cd semantica
-git remote add upstream https://github.com/Hawksight-AI/semantica.git
+git remote add upstream https://github.com/semantica-agi/semantica.git
 ```
 
 ### 2. Set Up Environment
@@ -181,6 +195,39 @@ pip install -e ".[dev]"
 pre-commit install
 ```
 
+### Pinned CI dependencies
+
+`requirements-ci.txt` pins every transitive dependency at exact versions so CI,
+security scans, and release builds install the same packages every run (the
+Python equivalent of `explorer/package-lock.json` + `npm ci`). It is a
+**separate build environment**: every package carries a SHA-256 hash
+(`--generate-hashes`), so installs are reproducible and supply-chain safe —
+never install into your local dev environment from it.
+
+Regenerate it after changing `pyproject.toml` dependencies:
+
+```bash
+pip install uv==0.12.1
+uv pip compile pyproject.toml --python-version 3.11 --extra all --generate-hashes -o requirements-ci.txt
+```
+
+The `all` extra is the repo's cross-platform dependency set (GPU extras like
+`faiss-gpu`/`cupy` are excluded and installed separately on Linux — see
+`pyproject.toml`). Keep the pinned `uv` version in sync with CI so regeneration
+is deterministic.
+
+CI's staleness check re-resolves with the committed lockfile as a constraint
+and compares version lines only: upstream package releases never fail CI —
+the lockfile changes only when `pyproject.toml` changes intentionally.
+
+CI fails if `requirements-ci.txt` is stale relative to `pyproject.toml`
+(the version-line comparison detects new/removed/changed dependencies).
+
+Build-system pins: `[build-system].requires` is pinned to exact versions
+(`setuptools==84.0.0`, `wheel==0.48.0`) and release builds run
+`python -m build --no-isolation` against the lockfile — no unpinned
+build-time isolation anywhere.
+
 ### 3. Create Branch
 
 ```bash
@@ -351,8 +398,8 @@ result = instance.method()
 ## 🆘 Getting Help
 
 - 💬 [Discord](https://discord.gg/sV34vps5hH) - Real-time chat
-- 💭 [GitHub Discussions](https://github.com/Hawksight-AI/semantica/discussions) - Q&A
-- 🐛 [GitHub Issues](https://github.com/Hawksight-AI/semantica/issues) - Bug reports
+- 💭 [GitHub Discussions](https://github.com/semantica-agi/semantica/discussions) - Q&A
+- 🐛 [GitHub Issues](https://github.com/semantica-agi/semantica/issues) - Bug reports
 
 **Before asking:** Check existing documentation, search issues/discussions, review cookbook examples
 
@@ -387,4 +434,4 @@ This project follows a [Code of Conduct](CODE_OF_CONDUCT.md). Be respectful and
 
 Every contribution matters - whether it's a single line of code, a typo fix, a helpful answer, or a bug report. We appreciate you! 🙏
 
-⭐ **Give us a Star** • 🍴 **[Fork Semantica](https://github.com/Hawksight-AI/semantica/fork)** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**
+⭐ **Give us a Star** • 🍴 **[Fork Semantica](https://github.com/semantica-agi/semantica/fork)** • 💬 **Join our [Discord](https://discord.gg/sV34vps5hH)**

CONTRIBUTORS.md

@@ -44,7 +44,7 @@ We recognize all types of contributions:
 All contributors are recognized in:
 
 - This contributors list
-- [GitHub contributors page](https://github.com/Hawksight-AI/semantica/graphs/contributors)
+- [GitHub contributors page](https://github.com/semantica-agi/semantica/graphs/contributors)
 - Release notes for significant contributions
 - Community appreciation
 
@@ -54,7 +54,7 @@ All contributors are recognized in:
 
 ### Automatic Recognition
 
-If you've made a commit, you'll automatically appear in [GitHub's contributors graph](https://github.com/Hawksight-AI/semantica/graphs/contributors).
+If you've made a commit, you'll automatically appear in [GitHub's contributors graph](https://github.com/semantica-agi/semantica/graphs/contributors).
 
 ### Using All-Contributors Bot
 
@@ -101,7 +101,7 @@ When using the all-contributors bot, use these codes:
 - `infra` - Infrastructure
 - `maintenance` - Maintenance
 
-See [all-contributors specification](https://allcontributors.org/docs/en/emoji-key) for complete list.
+See [all-contributors specification](https://github.com/all-contributors/all-contributors#emoji-key) for complete list.
 
 ---
 
@@ -111,4 +111,4 @@ Every contribution, no matter how small, helps make Semantica better. Thank you
 
 **Want to contribute?** 
 
-⭐ Give us a Star • 🍴 [Fork us](https://github.com/Hawksight-AI/semantica/fork) • Check out our [Contributing Guide](CONTRIBUTING.md) to get started!
+⭐ Give us a Star • 🍴 [Fork us](https://github.com/semantica-agi/semantica/fork) • Check out our [Contributing Guide](CONTRIBUTING.md) to get started!

Dockerfile

@@ -9,7 +9,7 @@ RUN npm ci
 COPY explorer/ ./
 RUN mkdir -p /app/semantica && npm run build
 
-FROM python:3.14-slim AS runtime
+FROM python:3.13-slim AS runtime
 
 ENV PYTHONDONTWRITEBYTECODE=1 \
     PYTHONUNBUFFERED=1 \

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2026 Hawksight AI
+Copyright (c) 2026 Semantica
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1 +1,2 @@
 recursive-include semantica/static *
+recursive-include semantica/ontology/vocabulary *.ttl

README.md

@@ -2,7 +2,15 @@
 
 <img src="Semantica Logo.png" alt="Semantica" width="420"/>
 
-<a href="https://trendshift.io/repositories/18986?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-18986" target="_blank" rel="noopener noreferrer"><img src="https://trendshift.io/api/badge/repositories/18986" alt="semantica-agi%2Fsemantica | Trendshift" width="250" height="55"/></a>
+<div style="display:flex; gap:10px; align-items:center; flex-wrap:wrap;">
+  <a href="https://trendshift.io/repositories/18986?utm_source=repository-badge&amp;utm_medium=badge&amp;utm_campaign=badge-repository-18986" target="_blank" rel="noopener noreferrer">
+    <img src="https://trendshift.io/api/badge/repositories/18986" alt="semantica-agi/semantica | Trendshift" width="250" height="55"/>
+  </a>
+
+  <a href="https://trendshift.io/repositories/18986?utm_source=trendshift-badge&amp;utm_medium=badge&amp;utm_campaign=badge-trendshift-18986" target="_blank" rel="noopener noreferrer">
+    <img src="https://trendshift.io/api/badge/trendshift/repositories/18986/weekly?language=Python" alt="semantica-agi/semantica | Trendshift" width="250" height="55"/>
+  </a>
+</div>
 
 ### Graph-Native Infrastructure for Context and Accountable AI Systems
 
@@ -52,6 +60,8 @@ Most AI agents act without a trail. They store embeddings, not meaning: context
 
 Semantica sits underneath your LLM, vector store, and agent framework as a deterministic infrastructure layer: no LLM required for graph construction, reasoning, or provenance.
 
+> ⚠️ **System-level explainability, not foundation-model explainability.** Semantica does not expose or reconstruct what happens *inside* the LLM — its internal reasoning or chain-of-thought stays opaque, as it does for any external system. Semantica explains what's *outside* the model: the context and data fed in, the decision produced, its provenance, relevant relationships, applied policies, and the full execution trail.
+
 **Who it's for:**
 
 - **AI/ML platform teams** shipping agents that make consequential decisions and need structured, queryable context built from fragmented raw data, not just a vector index
@@ -77,7 +87,7 @@ Semantica sits underneath your LLM, vector store, and agent framework as a deter
 - **Graph Analytics:** Centrality, community detection, link prediction, and shortest-path queries over the graph you just built
 - **Polyglot Graph Storage:** Native RDF (embedded Oxigraph, Blazegraph, Apache Jena, Eclipse RDF4J via SPARQL) and Labeled Property Graphs (Neo4j, FalkorDB, Apache AGE, AWS Neptune via Cypher), plus vector stores, all swappable without touching your code
 - **Visualization:** Explore any graph, ontology, or timeline in an interactive browser workbench
-- **Drop-in Integrations:** Native Agno support, a full-featured MCP server, a comprehensive CLI, a REST API, and plugins across major editors
+- **Drop-in Integrations:** Native Agno, CrewAI, and LangChain support, a full-featured MCP server, a comprehensive CLI, a REST API, and plugins across major editors
 
 ---
 
@@ -132,11 +142,13 @@ compliant = graph.check_decision_rules({"category": "vendor_selection"})  # poli
 ```bash
 semantica doctor
 # Python 3.11.9         pass
-# semantica 0.6.0       pass
+# semantica 0.6.7       pass
 # faiss vector store    pass
 # Config file           pass    ~/.semantica/config.yaml
 ```
 
+**Running in a script or CI?** Progress bars are written only when stdout is an interactive terminal (or a Jupyter notebook), so piping and redirecting stay clean by default. Override with `SEMANTICA_DISABLE_PROGRESS=1` to silence progress everywhere, or `SEMANTICA_FORCE_PROGRESS=1` to keep it when stdout is redirected. `SEMANTICA_DISABLE_PROGRESS` takes precedence.
+
 <div align="center">
 
 If Semantica solves a real problem for you, a star helps others find it.
@@ -293,17 +305,10 @@ graph.add_causal_relationship(d1, d2, relationship_type="CAUSED")
 prov.track_entity("patient_P4821", source="ehr/medication_orders_2024.json",
                   metadata={"extractor": "NamedEntityRecognizer"})
 
-# Export W3C PROV-O for regulator submission - RDFExporter expects
-# {"entities": [...], "relationships": [...]}, so map ContextGraph.to_dict()'s
-# {"nodes": [...], "edges": [...]} shape onto it first
-graph_dict = graph.to_dict()
-kg = {
-    "entities": [{"id": n["id"], "type": n["type"], "text": n["content"]} for n in graph_dict["nodes"]],
-    "relationships": [
-        {"source_id": e["source"], "target_id": e["target"], "type": e["type"]}
-        for e in graph_dict["edges"]
-    ],
-}
+# Export W3C PROV-O for regulator submission - to_kg_dict() is the official
+# adapter that emits the {"entities": [...], "relationships": [...]} /
+# source_id shape RDFExporter expects, so no manual field mapping is needed
+kg = graph.to_kg_dict()
 RDFExporter().export(kg, "audit_trail.ttl", format="turtle")
 ```
 
@@ -877,20 +882,14 @@ fact = BiTemporalFact(
     recorded_at=datetime(2024, 3, 5),
 )
 
-# Query facts valid within a time window - query_time_range() expects
-# {"relationships": [...]} with source_id/target_id keys, which differs from
-# ContextGraph.to_dict()'s {"nodes", "edges"} shape, so map it first
-graph_dict = graph.to_dict()
-kg_relationships = {
-    "relationships": [
-        {**e, "source_id": e["source"], "target_id": e["target"]}
-        for e in graph_dict["edges"]
-    ]
-}
+# Query facts valid within a time window - to_kg_dict() is the official
+# adapter that emits {"entities", "relationships"} with source_id/target_id
+# keys, the shape query_time_range() expects (no manual mapping required)
+kg = graph.to_kg_dict()
 
 tq = TemporalGraphQuery()
 facts_in_window = tq.query_time_range(
-    kg_relationships, query="valid_facts", start_time="2024-01-01", end_time="2024-12-31"
+    kg, query="valid_facts", start_time="2024-01-01", end_time="2024-12-31"
 )
 
 # Normalize natural language temporal expressions - returns a (start, end) range
@@ -1189,7 +1188,7 @@ Start with `semantica`, verify with `doctor`, build a graph, and explore the com
 
 ## Integrations
 
-Native plugin bundles for Claude Code, Cursor, Codex, Windsurf, Cline, Continue, VS Code, and OpenClaw; a full-featured MCP server for any MCP-compatible client; a comprehensive REST API; and first-class Agno support for multi-agent shared context. Every major LLM provider is already supported via `semantica.llms` and LiteLLM: OpenAI, Anthropic, Gemini, Mistral, Llama, Groq, Cohere, Azure, Bedrock, Ollama, DeepSeek, HuggingFace, and more.
+Native plugin bundles for Claude Code, Cursor, Codex, Windsurf, Cline, Continue, VS Code, and OpenClaw; a full-featured MCP server for any MCP-compatible client; a comprehensive REST API; and first-class Agno, CrewAI, and LangChain support for agentic frameworks. Every major LLM provider is already supported via `semantica.llms` and LiteLLM: OpenAI, Anthropic, Gemini, Mistral, Llama, Groq, Cohere, Azure, Bedrock, Ollama, DeepSeek, HuggingFace, and more.
 
 MCP setup takes 30 seconds — see [MCP Server](#mcp-server) below.
 
@@ -1303,27 +1302,27 @@ MCP setup takes 30 seconds — see [MCP Server](#mcp-server) below.
 <strong>Agno</strong><br/>
 <sub>First-class · <code>pip install semantica[agno]</code></sub>
 </td>
+<td align="center" width="12.5%">
+<a href="https://github.com/crewAIInc/crewAI"><img src="https://github.com/crewAIInc.png?size=120" alt="CrewAI" width="48" height="48" /></a><br/>
+<strong>CrewAI</strong><br/>
+<sub>First-class · <code>pip install semantica[crewai]</code></sub>
+</td>
+<td align="center" width="12.5%">
+<a href="https://github.com/langchain-ai/langchain"><img src="https://github.com/langchain-ai.png?size=120" alt="LangChain" width="48" height="48" /></a><br/>
+<strong>LangChain</strong><br/>
+<sub>First-class · <code>pip install semantica[langchain]</code></sub>
+</td>
 </tr>
 <tr>
 <th colspan="8" align="left">Already Supported via REST API &amp; MCP</th>
 </tr>
 <tr>
 <td align="center" width="12.5%">
-<a href="https://github.com/langchain-ai/langchain"><img src="https://github.com/langchain-ai.png?size=120" alt="LangChain" width="48" height="48" /></a><br/>
-<strong>LangChain</strong><br/>
-<sub>REST API · MCP</sub>
-</td>
-<td align="center" width="12.5%">
 <a href="https://github.com/langchain-ai/langgraph"><img src="https://github.com/langchain-ai.png?size=120" alt="LangGraph" width="48" height="48" /></a><br/>
 <strong>LangGraph</strong><br/>
 <sub>REST API · MCP</sub>
 </td>
 <td align="center" width="12.5%">
-<a href="https://github.com/crewAIInc/crewAI"><img src="https://github.com/crewAIInc.png?size=120" alt="CrewAI" width="48" height="48" /></a><br/>
-<strong>CrewAI</strong><br/>
-<sub>REST API · MCP</sub>
-</td>
-<td align="center" width="12.5%">
 <a href="https://github.com/run-llama/llama_index"><img src="https://github.com/run-llama.png?size=120" alt="LlamaIndex" width="48" height="48" /></a><br/>
 <strong>LlamaIndex</strong><br/>
 <sub>REST API · MCP</sub>
@@ -1349,16 +1348,6 @@ MCP setup takes 30 seconds — see [MCP Server](#mcp-server) below.
 </tr>
 <tr>
 <td align="center" width="12.5%">
-<a href="https://github.com/langchain-ai/langchain"><img src="https://github.com/langchain-ai.png?size=120" alt="LangChain" width="48" height="48" /></a><br/>
-<strong>LangChain</strong><br/>
-<sub>Dedicated toolkit</sub>
-</td>
-<td align="center" width="12.5%">
-<a href="https://github.com/crewAIInc/crewAI"><img src="https://github.com/crewAIInc.png?size=120" alt="CrewAI" width="48" height="48" /></a><br/>
-<strong>CrewAI</strong><br/>
-<sub>Dedicated toolkit</sub>
-</td>
-<td align="center" width="12.5%">
 <a href="https://github.com/run-llama/llama_index"><img src="https://github.com/run-llama.png?size=120" alt="LlamaIndex" width="48" height="48" /></a><br/>
 <strong>LlamaIndex</strong><br/>
 <sub>Dedicated toolkit</sub>
@@ -1474,12 +1463,18 @@ For contributor / dev-server setup: **[explorer/README.md: Local Setup Guide](ex
 
 ---
 
-## What's New in v0.6.0
+## What's New in v0.6.7
 
-- **Named-Graph Support for `JenaStore`:** Migrated onto `rdflib.Dataset(default_union=False)`, completing cross-backend named-graph parity across Blazegraph, RDF4J, and Jena; `add_triplets()` gains a `graph=` option
-- **SPARQL CONSTRUCT Query Templates:** Parameterized, injection-safe `CONSTRUCT` templates extended from Blazegraph-only to RDF4J and Jena, plus pipeline integration via the `construct_template` step type
-- **Databricks Connector:** `DatabricksIngestor` for Unity Catalog + Delta Lake ingestion, with PAT/OAuth M2M auth, table/query ingestion, and catalog/schema/table/lineage introspection. Install with `pip install "semantica[db-databricks]"`
-- **SQLite Vector Store Backend:** `SQLiteVecStore`, a disk-backed local vector store on `sqlite-vec`'s `vec0` virtual tables, with Cosine/L2 metrics, metadata filtering, and WAL mode. Install with `pip install semantica[vectorstore-sqlite]`
+**Feature release**, plus one SSRF hardening fix and a large batch of correctness fixes across the RDF/ontology export pipeline:
+
+- **First-class LangChain integration** (`semantica[langchain]`): a `BaseRetriever` and `VectorStore` over `HybridSearch`, plus graph/decision-query tools
+- **SAP OData ingestor** (`semantica[ingest-sap]`): OAuth2/Basic-auth, SSRF-guarded ingestion for Business Partners and Sales Orders, following the existing Snowflake/Databricks connector pattern
+- **`ContextGraph` gains deterministic, human-editable Markdown round-trip persistence** alongside the existing JSON API, and the Explorer graph inspector gains a read-only Markdown content viewer
+- **`reasoning` gains a structured Action layer**: rule-driven `Assert`/`Retract`/`Call`/`EmitEvent` actions with optional provenance, turning the reasoner into a production-rule system
+- **`run_shacl_validation` is now a public, documented API**, and a dozen ontology/RDF export correctness fixes land: OWL property/class export, SHACL target-namespace resolution, one canonical confidence datatype across all four RDF formats, reachable OWL-Time reification, JSON-LD default-graph and content-derived document identity, and full metadata passthrough on every RDF serializer
+- **Security**: Agno's `AgnoKnowledgeGraph.load_urls()` and OpenClaw's MCP tool now route outbound requests through the shared SSRF guard
+
+Also fixes: `PipelineBuilder.set_parallelism()` now actually parallelizes independent pipeline steps, `flatten_dict()` no longer silently drops data on a key collision, `Config.get()` honors boolean environment overrides, and the MCP server's `export_graph` tool works again on every format.
 
 → [Full release notes](RELEASE_NOTES.md) · [Changelog](CHANGELOG.md)
 
@@ -1497,6 +1492,8 @@ Semantica is designed for environments where AI outputs must be explainable, aud
 - **Cybersecurity:** Threat attribution, incident response timelines, and IOC provenance tracking
 - **Autonomous Systems:** Decision logs, safety validation, and explainable AI for certification
 
+> ⚠️ **This is system-level explainability, not foundation-model explainability.** Semantica does not expose, reconstruct, or explain what happens *inside* the LLM/foundation model — its internal reasoning or chain-of-thought stays opaque, as it does for any external system. What Semantica explains is *outside* the model: the context and data fed in, the decision produced, its provenance, the relevant relationships, the policies applied, and the full execution trail. In short, Semantica explains and audits what the AI system did, not the LLM's private internal reasoning.
+
 ---
 
 ## Installation
@@ -1508,6 +1505,8 @@ pip install semantica[all]      # everything
 
 ```bash
 pip install semantica[agno]                 # Agno multi-agent integration
+pip install semantica[crewai]               # CrewAI integration
+pip install semantica[langchain]            # LangChain / LangGraph integration
 pip install semantica[llm-litellm]          # OpenAI, Anthropic, Gemini, Mistral, Llama, Groq, Cohere, Bedrock, Ollama, DeepSeek, and more
 pip install semantica[graph-neo4j]          # Neo4j graph store (LPG)
 pip install semantica[graph-falkordb]       # FalkorDB graph store (LPG)
@@ -1560,11 +1559,11 @@ On-premises deployment · Private cloud · Custom domain implementations · SLA-
 
 ## Star History
 
-<a href="https://www.star-history.com/?repos=semantica-agi%2Fsemantica&type=date&legend=top-left">
+<a href="https://star-history.dera.page/#semantica-agi/semantica&amp;type=date&amp;legend=top-left">
  <picture>
-   <source media="(prefers-color-scheme: dark)" srcset="https://api.star-history.com/chart?repos=semantica-agi/semantica&type=date&theme=dark&legend=top-left" />
-   <source media="(prefers-color-scheme: light)" srcset="https://api.star-history.com/chart?repos=semantica-agi/semantica&type=date&legend=top-left" />
-   <img alt="Star History Chart" src="https://api.star-history.com/chart?repos=semantica-agi/semantica&type=date&legend=top-left" />
+   <source media="(prefers-color-scheme: dark)" srcset="https://star-history.dera.page/svg?repos=semantica-agi/semantica&amp;type=date&amp;theme=dark&amp;legend=top-left" />
+   <source media="(prefers-color-scheme: light)" srcset="https://star-history.dera.page/svg?repos=semantica-agi/semantica&amp;type=date&amp;legend=top-left" />
+   <img alt="Star History Chart" src="https://star-history.dera.page/svg?repos=semantica-agi/semantica&amp;type=date&amp;legend=top-left" />
  </picture>
 </a>
 
@@ -1593,6 +1592,23 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for full guidelines.
 
 ---
 
+## Cite Us
+
+If you use Semantica in your research or production systems, please cite it as:
+
+```bibtex
+@software{semantica2026,
+  title  = {Semantica: Graph-Native Infrastructure for Context and Accountable AI Systems},
+  author = {Semantica},
+  year   = {2026},
+  url    = {https://github.com/semantica-agi/semantica}
+}
+```
+
+All citation formats (APA, MLA, Chicago, IEEE) live on the [Citation](https://docs.getsemantica.ai/citation) page — every format attributes authorship to **Semantica**, not individual contributors.
+
+---
+
 <div align="center">
 
 MIT License · Built by [Semantica](https://github.com/semantica-agi)

cookbook/advanced/01_Advanced_Extraction.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/01_Advanced_Extraction.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/01_Advanced_Extraction.ipynb)\n",
     "\n",
     "# Advanced Extraction\n",
     "\n",

cookbook/advanced/03_Complete_Visualization_Suite.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/03_Complete_Visualization_Suite.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/03_Complete_Visualization_Suite.ipynb)\n",
     "\n",
     "# Complete Visualization Suite\n",
     "\n",

cookbook/advanced/05_Multi_Format_Export.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/05_Multi_Format_Export.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/05_Multi_Format_Export.ipynb)\n",
     "\n",
     "# Advanced Multi-Format Export\n",
     "\n",

cookbook/advanced/08_Reasoning_and_Inference.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/08_Reasoning_and_Inference.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/08_Reasoning_and_Inference.ipynb)\n",
     "\n",
     "# Reasoning and Inference\n",
     "\n",

cookbook/advanced/09_Semantic_Layer_Construction.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/09_Semantic_Layer_Construction.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/09_Semantic_Layer_Construction.ipynb)\n",
     "\n",
     "# Semantic Layer Construction\n",
     "\n",

cookbook/advanced/10_Temporal_Knowledge_Graphs.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/10_Temporal_Knowledge_Graphs.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/10_Temporal_Knowledge_Graphs.ipynb)\n",
     "\n",
     "# Deep Dive: Temporal Knowledge Graphs\n",
     "\n",

cookbook/advanced/12_Unstructured_to_Ontology.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/12_Unstructured_to_Ontology.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/12_Unstructured_to_Ontology.ipynb)\n",
     "\n",
     "# Unstructured Text to Ontology\n",
     "\n",

cookbook/advanced/13_Manual_Ontology_Snowflake_Mapping.ipynb

@@ -18,7 +18,7 @@
    "id": "cell-0",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/13_Manual_Ontology_Snowflake_Mapping.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/13_Manual_Ontology_Snowflake_Mapping.ipynb)\n",
     "\n",
     "# Manual Ontology + Snowflake Mapping\n",
     "\n",

cookbook/advanced/14_Datalog_Style_Reasoning.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/14_Datalog_Style_Reasoning.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/14_Datalog_Style_Reasoning.ipynb)\n",
     "\n",
     "# Datalog-Style Reasoning\n",
     "\n",

cookbook/advanced/Advanced_Vector_Store_and_Search.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/advanced/Advanced_Vector_Store_and_Search.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/advanced/Advanced_Vector_Store_and_Search.ipynb)\n",
     "\n",
     "# Advanced Vector Store - Made Easy\n",
     "\n",
@@ -352,7 +352,7 @@
     "- Build a multi-user application\n",
     "- Explore the [introduction notebook](../introduction/13_Vector_Store.ipynb) for more basics\n",
     "\n",
-    "**Need Help?** Check our [documentation](https://semantica.readthedocs.io) or ask on [GitHub](https://github.com/Hawksight-AI/semantica)."
+    "**Need Help?** Check our [documentation](https://semantica.readthedocs.io) or ask on [GitHub](https://github.com/semantica-agi/semantica)."
    ]
   }
  ],

cookbook/introduction/01_Welcome_to_Semantica.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/01_Welcome_to_Semantica.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/01_Welcome_to_Semantica.ipynb)\n",
     "\n",
     "Semantica is a **semantic intelligence and knowledge engineering framework**. It helps you:\n",
     "\n",

cookbook/introduction/02_Data_Ingestion.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/02_Data_Ingestion.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/02_Data_Ingestion.ipynb)\n",
     "\n",
     "# Data Ingestion - Comprehensive Guide\n",
     "\n",

cookbook/introduction/03_Document_Parsing.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/04_Document_Parsing.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/03_Document_Parsing.ipynb)\n",
     "\n",
     "# Document Parsing\n",
     "\n",

cookbook/introduction/04_Data_Normalization.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/05_Data_Normalization.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/04_Data_Normalization.ipynb)\n",
     "\n",
     "# Data Normalization\n",
     "\n",

cookbook/introduction/05_Entity_Extraction.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/05_Entity_Extraction.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/05_Entity_Extraction.ipynb)\n",
     "\n",
     "#  Entity Extraction - Comprehensive Guide\n",
     "\n",
@@ -622,7 +622,7 @@
     "\n",
     "---\n",
     "\n",
-    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/Hawksight-AI/semantica) or [documentation](https://semantica.readthedocs.io)."
+    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/semantica-agi/semantica) or [documentation](https://semantica.readthedocs.io)."
    ]
   }
  ],

cookbook/introduction/06_Relation_Extraction.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/06_Relation_Extraction.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/06_Relation_Extraction.ipynb)\n",
     "\n",
     "#  Relation Extraction - Comprehensive Guide\n",
     "\n",
@@ -599,7 +599,7 @@
     "\n",
     "---\n",
     "\n",
-    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/Hawksight-AI/semantica) or [documentation](https://semantica.readthedocs.io)."
+    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/semantica-agi/semantica) or [documentation](https://semantica.readthedocs.io)."
    ]
   }
  ],

cookbook/introduction/07_Building_Knowledge_Graphs.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/08_Building_Knowledge_Graphs.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/07_Building_Knowledge_Graphs.ipynb)\n",
     "\n",
     "# Building Knowledge Graphs\n",
     "\n",

cookbook/introduction/08_Your_First_Knowledge_Graph.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/09_Your_First_Knowledge_Graph.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/08_Your_First_Knowledge_Graph.ipynb)\n",
     "\n",
     "# 🚀 Your First Knowledge Graph\n",
     "\n",

cookbook/introduction/10_Graph_Analytics.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/11_Graph_Analytics.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/10_Graph_Analytics.ipynb)\n",
     "\n",
     "# Graph Analytics\n",
     "\n",

cookbook/introduction/11_Chunking_and_Splitting.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/11_Chunking_and_Splitting.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/11_Chunking_and_Splitting.ipynb)\n",
     "\n",
     "# Chunking and Splitting - Comprehensive Guide\n",
     "\n",
@@ -817,7 +817,7 @@
     "\n",
     "---\n",
     "\n",
-    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/Hawksight-AI/semantica) or [documentation](https://semantica.readthedocs.io)."
+    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/semantica-agi/semantica) or [documentation](https://semantica.readthedocs.io)."
    ]
   }
  ],

cookbook/introduction/12_Embedding_Generation.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/13_Embedding_Generation.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/12_Embedding_Generation.ipynb)\n",
     "\n",
     "# Embedding Generation\n",
     "\n",

cookbook/introduction/13_Vector_Store.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/13_Vector_Store.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/13_Vector_Store.ipynb)\n",
     "\n",
     "# Vector Store - Comprehensive Guide\n",
     "\n",
@@ -492,7 +492,7 @@
     "\n",
     "---\n",
     "\n",
-    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/Hawksight-AI/semantica) or [documentation](https://semantica.readthedocs.io)."
+    "**Questions or Issues?** Check out our [GitHub repository](https://github.com/semantica-agi/semantica) or [documentation](https://semantica.readthedocs.io)."
    ]
   }
  ],

cookbook/introduction/14_Ontology.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/14_Ontology.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/14_Ontology.ipynb)\n",
     "\n",
     "#  Ontology Generation \n",
     "\n",

cookbook/introduction/15_Export.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/15_Export.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/15_Export.ipynb)\n",
     "\n",
     "# Export Module - Comprehensive Guide\n",
     "\n",

cookbook/introduction/16_Visualization.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/17_Visualization.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/16_Visualization.ipynb)\n",
     "\n",
     "# Visualization\n",
     "\n",

cookbook/introduction/18_Deduplication.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/18_Deduplication.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/18_Deduplication.ipynb)\n",
     "\n",
     "# Deduplication in Semantica\n",
     "\n",

cookbook/introduction/19_Context_Module.ipynb

@@ -5,7 +5,7 @@
    "id": "c21e9c8d",
    "metadata": {},
    "source": [
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Hawksight-AI/semantica/blob/main/cookbook/introduction/19_Context_Module.ipynb)\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/19_Context_Module.ipynb)\n",
     "\n",
     "# Context Module — Practical Guide\n",
     "\n",

cookbook/introduction/22_Provenance_Tracking.ipynb

@@ -0,0 +1,253 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Provenance Tracking (W3C PROV-O)\n",
+    "\n",
+    "## Overview\n",
+    "\n",
+    "In high-stakes domains — healthcare, legal, finance, research — a Knowledge Graph is only as trustworthy as its ability to answer **\"where did this fact come from?\"**. Semantica's `provenance` module provides audit-grade, W3C PROV-O-aligned tracking for every entity, relationship and chunk that flows through your pipeline.\n",
+    "\n",
+    "In this cookbook you will learn how to:\n",
+    "\n",
+    "- Track entities and relationships with **source details** (DOI, page, verbatim quote, confidence)\n",
+    "- Walk the full **lineage** of a fact (document → chunk → entity → KG)\n",
+    "- Audit **revision history** and **all sources** behind an entity\n",
+    "- **Invalidate** a fact without deleting it (prov:Invalidation) — corrections stay provable\n",
+    "- Verify **tamper-evidence** with chained SHA-256 checksums\n",
+    "\n",
+    "**The Scenario:** a research team ingests findings from two scientific papers (with DOIs) into a Knowledge Graph. A regulator later asks: *\"Which paper, which figure, and which exact sentence supports the claim that fish biomass increased by 463%? And was that fact ever corrected?\"*"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip install -q semantica"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import json\n",
+    "from semantica.provenance import (\n",
+    "    ProvenanceManager,\n",
+    "    compute_checksum,\n",
+    "    verify_checksum,\n",
+    ")\n",
+    "\n",
+    "# In-memory storage for this demo; pass storage_path=\"provenance.db\"\n",
+    "# (or a config with provenance.storage_path) for a persistent SQLite backend.\n",
+    "prov = ProvenanceManager()\n",
+    "print(\"ProvenanceManager ready (in-memory storage)\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 1: Track Entities with Audit-Grade Source Details\n",
+    "\n",
+    "Every fact we ingest carries its evidence with it: the **source identifier** (a DOI here), the **location** inside the source (a figure), the **verbatim quote**, and the extractor's **confidence**."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Finding from paper #1\n",
+    "entry_biomass = prov.track_entity(\n",
+    "    entity_id=\"claim_biomass_increase\",\n",
+    "    source=\"DOI:10.1371/journal.pone.0023601\",\n",
+    "    confidence=0.92,\n",
+    "    source_location=\"Figure 2\",\n",
+    "    source_quote=\"Total fish biomass increased by 463% ...\",\n",
+    ")\n",
+    "\n",
+    "# Supporting entity from paper #2\n",
+    "entry_reserve = prov.track_entity(\n",
+    "    entity_id=\"marine_reserve_1\",\n",
+    "    source=\"DOI:10.1126/science.1088121\",\n",
+    "    confidence=0.88,\n",
+    "    source_location=\"Table 1\",\n",
+    "    source_quote=\"... no-take marine reserve at Cabo Pulmo ...\",\n",
+    ")\n",
+    "\n",
+    "print(\"Tracked:\", entry_biomass.entity_id, \"|\", entry_reserve.entity_id)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 2: Track the Relationship Between Facts\n",
+    "\n",
+    "Facts rarely stand alone. The claim about biomass increase is *about* the marine reserve — that relationship is a first-class provenance-tracked object too.\n",
+    "\n",
+    "`track_relationship()` has no dedicated subject/object fields, so by convention we record which two entities it connects inside `metadata`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rel = prov.track_relationship(\n",
+    "    relationship_id=\"rel_biomass_about_reserve\",\n",
+    "    source=\"DOI:10.1371/journal.pone.0023601\",\n",
+    "    metadata={\n",
+    "        \"type\": \"measured_at\",\n",
+    "        # No dedicated endpoint fields on track_relationship() yet -- record\n",
+    "        # which entities this relationship connects here by convention.\n",
+    "        \"subject_entity_id\": \"claim_biomass_increase\",\n",
+    "        \"object_entity_id\": \"marine_reserve_1\",\n",
+    "    },\n",
+    ")\n",
+    "\n",
+    "print(\"Relationship tracked:\", rel.entity_id, \"|\", rel.metadata[\"subject_entity_id\"], \"->\", rel.metadata[\"object_entity_id\"])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 3: Walk the Lineage\n",
+    "\n",
+    "`get_lineage` reconstructs everything known about a fact; `trace_lineage` returns the ordered chain of `ProvenanceEntry` records — every version, every activity, every agent that touched it."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lineage = prov.get_lineage(\"claim_biomass_increase\")\n",
+    "print(json.dumps(lineage, indent=2, default=str)[:800])\n",
+    "\n",
+    "print(\"\\n--- ordered chain ---\")\n",
+    "for e in prov.trace_lineage(\"claim_biomass_increase\"):\n",
+    "    print(f\"{e.entity_id} | seq#{e.sequence_id} | {e.activity_id}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 4: Audit Sources and Revision History\n",
+    "\n",
+    "When the regulator asks *\"has this fact ever been corrected?\"*, `revision_history` answers with the full version chain, and `get_all_sources` lists every source document that ever supported the entity."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "revisions = prov.revision_history(\"claim_biomass_increase\")\n",
+    "print(f\"{len(revisions)} revision(s) on record\")\n",
+    "\n",
+    "for s in prov.get_all_sources(\"claim_biomass_increase\"):\n",
+    "    print(\"source:\", s)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 5: Invalidate — Correct Without Deleting\n",
+    "\n",
+    "Suppose paper #1 is retracted in part. An audit trail must **not** silently delete the fact: `invalidate` archives the pre-invalidation state and appends a fresh `prov:Invalidation` entry naming **who** retracted it and **why**."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "invalidated = prov.invalidate(\n",
+    "    entity_id=\"claim_biomass_increase\",\n",
+    "    agent_id=\"reviewer_dr_chen\",\n",
+    "    reason=\"Partial retraction: Figure 2 statistics corrected by publisher (see erratum).\",\n",
+    ")\n",
+    "print(\"Invalidated:\", invalidated.entity_id, \"| invalidated flag:\", getattr(invalidated, \"invalidated\", True))\n",
+    "\n",
+    "stats = prov.get_statistics()\n",
+    "print(\"\\nStorage statistics:\", json.dumps(stats, indent=2, default=str))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 6: Verify Tamper-Evidence\n",
+    "\n",
+    "Each entry carries a deterministic SHA-256 checksum chained to the previous entry. Recompute and compare to detect any after-the-fact corruption of the provenance record."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# entry_biomass was returned by track_entity in Step 1\n",
+    "ok = verify_checksum(entry_biomass)\n",
+    "print(\"Checksum verified:\", ok)\n",
+    "\n",
+    "print(\"Computed:\", compute_checksum(entry_biomass)[:16], \"...\")\n",
+    "print(\"Stored:  \", entry_biomass.checksum[:16] if getattr(entry_biomass, 'checksum', None) else \"(see entry fields)\")\n",
+    "chain = prov.verify_chain()\n",
+    "print(\"Chain verification:\", json.dumps(chain, default=str)[:200])\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Summary\n",
+    "\n",
+    "| Need | Call |\n",
+    "|---|---|\n",
+    "| Record a fact's evidence | `prov.track_entity(entity_id, source, confidence=..., source_location=..., source_quote=...)` |\n",
+    "| Record a relationship | `prov.track_relationship(relationship_id, source, metadata=...)` |\n",
+    "| Full lineage of a fact | `prov.get_lineage(entity_id)` / `prov.trace_lineage(entity_id)` |\n",
+    "| \"Was it ever corrected?\" | `prov.revision_history(entity_id)` |\n",
+    "| \"Which sources support it?\" | `prov.get_all_sources(entity_id)` |\n",
+    "| Retract without deleting | `prov.invalidate(entity_id, agent_id, reason=...)` |\n",
+    "| Tamper check | `verify_checksum(entry)` |\n",
+    "\n",
+    "### Where to go next\n",
+    "\n",
+    "- **Conflict Detection and Resolution** (notebook 17) — what happens when two sources disagree.\n",
+    "- **Your First Knowledge Graph** (notebook 08) — plug `provenance=True` into extractors so tracking happens automatically during ingestion.\n",
+    "- The module docstring (`help(semantica.provenance)`) documents opt-in integration with `kg`, `split` and `conflicts` trackers."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.11"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

cookbook/introduction/23_Reasoning.ipynb

@@ -0,0 +1,383 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b76a5997",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/23_Reasoning.ipynb)\n",
+    "\n",
+    "# Reasoning Module — Practical Guide\n",
+    "\n",
+    "Semantica's `reasoning` module derives new knowledge from existing facts and knowledge graphs. It ships several strategies behind one facade:\n",
+    "\n",
+    "- **`Reasoner`** — unified facade with forward chaining, backward chaining, and one-shot `infer_facts`\n",
+    "- **`DatalogReasoner`** — semi-naive Datalog fixpoint evaluation with variable queries\n",
+    "- **`ExplanationGenerator`** — human-readable explanations and reasoning paths for inferred conclusions\n",
+    "- Plus lower-level engines: `ReteEngine`, `SPARQLReasoner`, `GraphReasoner`, temporal reasoning\n",
+    "\n",
+    "This notebook walks through the facade, the Datalog engine, and explanations. All APIs are verified against `semantica/reasoning/`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "52073af7",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:45:55.427457Z",
+     "iopub.status.busy": "2026-08-26T18:45:55.427247Z",
+     "iopub.status.idle": "2026-08-26T18:45:57.266607Z",
+     "shell.execute_reply": "2026-08-26T18:45:57.264783Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!pip install -q semantica"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "06deb916",
+   "metadata": {},
+   "source": [
+    "## 1) Forward chaining with the `Reasoner` facade\n",
+    "\n",
+    "Facts are simple `Predicate(args)` strings. Rules use `IF <conditions> THEN <conclusion>` with `?x`-style variables. `forward_chain()` derives everything possible and returns a list of `InferenceResult` objects."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "519ca92d",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:45:57.270791Z",
+     "iopub.status.busy": "2026-08-26T18:45:57.270352Z",
+     "iopub.status.idle": "2026-08-26T18:45:59.991941Z",
+     "shell.execute_reply": "2026-08-26T18:45:59.990678Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div style='font-family: monospace;'><h4>🧠 Semantica - 📊 Current Progress</h4><table style='width: 100%; border-collapse: collapse;'><tr><th>Status</th><th>Action</th><th>Module</th><th>Submodule</th><th>Progress</th><th>ETA</th><th>Rate</th><th>Time</th><th>Extracted</th></tr><tr><td>✅</td><td>Semantica is reasoning</td><td>🤔 reasoning</td><td>Reasoner</td><td>100.0%</td><td>-</td><td>-</td><td>0.00s</td><td>-</td></tr><tr><td>✅</td><td>Semantica is reasoning</td><td>🤔 reasoning</td><td>DatalogReasoner</td><td>100.0%</td><td>-</td><td>-</td><td>0.00s</td><td>-</td></tr><tr><td>✅</td><td>Semantica is reasoning</td><td>🤔 reasoning</td><td>ExplanationGenerator</td><td>100.0%</td><td>-</td><td>-</td><td>0.00s</td><td>-</td></tr></table></div>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "🔄 Semantica is reasoning: Performing forward chaining 🤔 reasoning Reasoner |░░░░░░░░░░░░░░░| 0.0% ETA: - Rate: - Time: 0.00s Extracted: -"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Inferred 2 new facts\n",
+      "  Human(Jane)  (rule: Rule 1, confidence: 1.0)\n",
+      "  Human(John)  (rule: Rule 1, confidence: 1.0)\n"
+     ]
+    }
+   ],
+   "source": [
+    "from semantica.reasoning import Reasoner\n",
+    "\n",
+    "reasoner = Reasoner()\n",
+    "\n",
+    "reasoner.add_fact(\"Person(John)\")\n",
+    "reasoner.add_fact(\"Person(Jane)\")\n",
+    "reasoner.add_rule(\"IF Person(?x) THEN Human(?x)\")\n",
+    "\n",
+    "results = reasoner.forward_chain()\n",
+    "print(f\"Inferred {len(results)} new facts\")\n",
+    "for res in results:\n",
+    "    print(f\"  {res.conclusion}  (rule: {res.rule_used.name}, confidence: {res.confidence})\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c1131c45",
+   "metadata": {},
+   "source": [
+    "## 2) One-shot inference with `infer_facts`\n",
+    "\n",
+    "`infer_facts(facts, rules)` **adds** the given facts and rules to this `Reasoner` instance, runs forward chaining to fixpoint, and returns the derived facts as strings. It does not reset the instance's existing state — create a fresh `Reasoner()` first if you need isolation between runs."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "26249990",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:45:59.995447Z",
+     "iopub.status.busy": "2026-08-26T18:45:59.995069Z",
+     "iopub.status.idle": "2026-08-26T18:46:00.004107Z",
+     "shell.execute_reply": "2026-08-26T18:46:00.002873Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['Employee(Jane, Acme)', 'Employee(John, Acme)']"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from semantica.reasoning import Reasoner\n",
+    "\n",
+    "derived = Reasoner().infer_facts(\n",
+    "    facts=[\"WorksFor(John, Acme)\", \"WorksFor(Jane, Acme)\"],\n",
+    "    rules=[\"IF WorksFor(?x, ?y) THEN Employee(?x, ?y)\"],\n",
+    ")\n",
+    "derived"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d5504a38",
+   "metadata": {},
+   "source": [
+    "## 3) Backward chaining: proving a goal\n",
+    "\n",
+    "`backward_chain(goal)` works backwards from a conclusion through the rules. It returns the `InferenceResult` that proves the goal, or `None`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "c4ef85dd",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:00.007740Z",
+     "iopub.status.busy": "2026-08-26T18:46:00.007346Z",
+     "iopub.status.idle": "2026-08-26T18:46:00.015561Z",
+     "shell.execute_reply": "2026-08-26T18:46:00.014145Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Human(John)\n",
+      "premises: ['Person(John)']\n"
+     ]
+    }
+   ],
+   "source": [
+    "from semantica.reasoning import Reasoner\n",
+    "\n",
+    "reasoner = Reasoner()\n",
+    "reasoner.add_fact(\"Person(John)\")\n",
+    "reasoner.add_rule(\"IF Person(?x) THEN Human(?x)\")\n",
+    "\n",
+    "proof = reasoner.backward_chain(\"Human(John)\")\n",
+    "print(proof.conclusion if proof else \"not provable\")\n",
+    "print(\"premises:\", proof.premises if proof else None)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b245581d",
+   "metadata": {},
+   "source": [
+    "## 4) Re-run safety\n",
+    "\n",
+    "`add_rule` deduplicates rules with identical conditions and conclusion, so re-executing a setup cell (the common Jupyter re-run) does not duplicate rules — see issue #732."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "fb2aeb39",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:00.019091Z",
+     "iopub.status.busy": "2026-08-26T18:46:00.018881Z",
+     "iopub.status.idle": "2026-08-26T18:46:00.024042Z",
+     "shell.execute_reply": "2026-08-26T18:46:00.022836Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Skipping duplicate rule (same conditions/conclusion as 'rule_1'): IF Person(?x) THEN Human(?x)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "1"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from semantica.reasoning import Reasoner\n",
+    "\n",
+    "reasoner = Reasoner()\n",
+    "reasoner.add_fact(\"Person(John)\")\n",
+    "\n",
+    "# Simulate a Jupyter cell re-run: add the same rule twice\n",
+    "r1 = reasoner.add_rule(\"IF Person(?x) THEN Human(?x)\")\n",
+    "r2 = reasoner.add_rule(\"IF Person(?x) THEN Human(?x)\")\n",
+    "\n",
+    "len(reasoner.rules)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ba2e5c4a",
+   "metadata": {},
+   "source": [
+    "## 5) Datalog reasoning\n",
+    "\n",
+    "`DatalogReasoner` uses classic Datalog syntax (`head :- body.`) and semi-naive fixpoint evaluation. Queries return variable bindings as a list of dicts — use uppercase variables to ask *which* facts hold."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "9ec5c0c4",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:00.026769Z",
+     "iopub.status.busy": "2026-08-26T18:46:00.026588Z",
+     "iopub.status.idle": "2026-08-26T18:46:00.034963Z",
+     "shell.execute_reply": "2026-08-26T18:46:00.032672Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[{'X': 'tom', 'Z': 'ann'}]"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from semantica.reasoning import DatalogReasoner\n",
+    "\n",
+    "datalog = DatalogReasoner()\n",
+    "datalog.add_fact(\"parent(tom, mary)\")\n",
+    "datalog.add_fact(\"parent(mary, ann)\")\n",
+    "datalog.add_rule(\"grandparent(X, Z) :- parent(X, Y), parent(Y, Z)\")\n",
+    "\n",
+    "datalog.derive_all()\n",
+    "datalog.query(\"grandparent(X, Z)\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d4f0689b",
+   "metadata": {},
+   "source": [
+    "## 6) Explanations for inferred conclusions\n",
+    "\n",
+    "`ExplanationGenerator` turns `InferenceResult` objects into structured `Explanation` and `ReasoningPath` records, so agents can show *why* they believe a derived fact."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "19dcd3a7",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:00.038649Z",
+     "iopub.status.busy": "2026-08-26T18:46:00.038396Z",
+     "iopub.status.idle": "2026-08-26T18:46:00.059188Z",
+     "shell.execute_reply": "2026-08-26T18:46:00.057805Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('Explanation', 'ReasoningPath')"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from semantica.reasoning import Reasoner, ExplanationGenerator\n",
+    "\n",
+    "reasoner = Reasoner()\n",
+    "reasoner.add_fact(\"Person(John)\")\n",
+    "reasoner.add_rule(\"IF Person(?x) THEN Human(?x)\")\n",
+    "results = reasoner.forward_chain()\n",
+    "\n",
+    "gen = ExplanationGenerator()\n",
+    "explanation = gen.generate_explanation(results[0])\n",
+    "path = gen.show_reasoning_path(results[0])\n",
+    "\n",
+    "type(explanation).__name__, type(path).__name__"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fb882ee4",
+   "metadata": {},
+   "source": [
+    "## Summary\n",
+    "\n",
+    "| Task | API |\n",
+    "|---|---|\n",
+    "| Derive all new facts | `Reasoner.forward_chain()` |\n",
+    "| One-shot inference | `Reasoner.infer_facts(facts, rules)` |\n",
+    "| Prove a goal | `Reasoner.backward_chain(goal)` |\n",
+    "| Datalog fixpoint | `DatalogReasoner.derive_all()` + `query(\"p(X, Y)\")` |\n",
+    "| Explain a conclusion | `ExplanationGenerator.generate_explanation(result)` |\n",
+    "\n",
+    "See also `semantica/reasoning/reasoning_usage.md` and the module docstrings for `ReteEngine`, `SPARQLReasoner`, and temporal reasoning."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

cookbook/introduction/24_Change_Management.ipynb

@@ -0,0 +1,299 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "8d7096ea",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/24_Change_Management.ipynb)\n",
+    "\n",
+    "# Change Management — Practical Guide\n",
+    "\n",
+    "Semantica's `change_management` module provides versioning, audit trails, and data-integrity checks for knowledge graphs and ontologies:\n",
+    "\n",
+    "- **`ChangeLogEntry`** — standardized change metadata (validated timestamp/author)\n",
+    "- **`InMemoryVersionStorage` / `SQLiteVersionStorage`** — version snapshot storage with named tags\n",
+    "- **`compute_checksum` / `verify_checksum`** — SHA-256 integrity verification\n",
+    "\n",
+    "This notebook runs a complete save → tag → verify → tamper-detect cycle. All outputs are real executed results verified against the repository's `semantica/change_management/` source at the time of writing (the `pip install` cell may fetch a newer release with slightly different behavior)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "7bdffec1",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:37.171333Z",
+     "iopub.status.busy": "2026-08-26T18:46:37.171183Z",
+     "iopub.status.idle": "2026-08-26T18:46:39.060860Z",
+     "shell.execute_reply": "2026-08-26T18:46:39.059594Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!pip install -q semantica"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "169efee1",
+   "metadata": {},
+   "source": [
+    "## 1) A `ChangeLogEntry` records *who* changed *what*, *when*\n",
+    "\n",
+    "`author` must be a valid email — the dataclass validates on construction (`ValidationError` otherwise), which keeps audit trails clean."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "5b17acdb",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:39.064077Z",
+     "iopub.status.busy": "2026-08-26T18:46:39.063818Z",
+     "iopub.status.idle": "2026-08-26T18:46:39.321881Z",
+     "shell.execute_reply": "2026-08-26T18:46:39.321036Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "ChangeLogEntry(timestamp='2026-08-15T09:00:00Z', author='demo@example.com', description='initial version', change_id=None, related_changes=[])"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from semantica.change_management import ChangeLogEntry\n",
+    "\n",
+    "entry = ChangeLogEntry(\n",
+    "    timestamp=\"2026-08-15T09:00:00Z\",\n",
+    "    author=\"demo@example.com\",\n",
+    "    description=\"initial version\",\n",
+    ")\n",
+    "entry"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "53d8df5c",
+   "metadata": {},
+   "source": [
+    "## 2) Save a versioned snapshot\n",
+    "\n",
+    "A snapshot is a dict with a required `label` plus your payload. Here we attach the KG data, the change log, and a SHA-256 `checksum` computed over everything except the checksum field itself."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "fec16f24",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:39.325528Z",
+     "iopub.status.busy": "2026-08-26T18:46:39.325140Z",
+     "iopub.status.idle": "2026-08-26T18:46:39.331480Z",
+     "shell.execute_reply": "2026-08-26T18:46:39.330586Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from semantica.change_management import InMemoryVersionStorage, compute_checksum\n",
+    "\n",
+    "storage = InMemoryVersionStorage()\n",
+    "\n",
+    "snapshot = {\n",
+    "    \"label\": \"v1.0.0\",\n",
+    "    \"data\": {\"entities\": {\"acme\": {\"type\": \"Company\"}}},\n",
+    "    \"change_log\": {\n",
+    "        \"timestamp\": entry.timestamp,\n",
+    "        \"author\": entry.author,\n",
+    "        \"description\": entry.description,\n",
+    "    },\n",
+    "}\n",
+    "snapshot[\"checksum\"] = compute_checksum({k: v for k, v in snapshot.items() if k != \"checksum\"})\n",
+    "\n",
+    "storage.save(snapshot)\n",
+    "storage.exists(\"v1.0.0\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0f1c603b",
+   "metadata": {},
+   "source": [
+    "## 3) Named tags pin a version for releases\n",
+    "\n",
+    "`save_tag` / `get_tag` map stable names (e.g. `release`) to version labels, decoupling consumers from label churn."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "62f7643e",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:39.335182Z",
+     "iopub.status.busy": "2026-08-26T18:46:39.334886Z",
+     "iopub.status.idle": "2026-08-26T18:46:39.339586Z",
+     "shell.execute_reply": "2026-08-26T18:46:39.338568Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('v1.0.0', ['v1.0.0'])"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "storage.save_tag(\"release\", \"v1.0.0\")\n",
+    "\n",
+    "storage.get_tag(\"release\"), [s[\"label\"] for s in storage.list_all()]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "96df12da",
+   "metadata": {},
+   "source": [
+    "## 4) Verify integrity — and catch tampering\n",
+    "\n",
+    "`verify_checksum(snapshot)` recomputes the SHA-256 over the snapshot (minus its `checksum` field) and compares. A single mutated character in the data flips the result to `False`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "26d0de85",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:39.342653Z",
+     "iopub.status.busy": "2026-08-26T18:46:39.342466Z",
+     "iopub.status.idle": "2026-08-26T18:46:39.346714Z",
+     "shell.execute_reply": "2026-08-26T18:46:39.345623Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "intact: True\n",
+      "tampered: False\n"
+     ]
+    }
+   ],
+   "source": [
+    "from semantica.change_management import verify_checksum\n",
+    "\n",
+    "stored = storage.get(\"v1.0.0\")\n",
+    "print(\"intact:\", verify_checksum(stored))\n",
+    "\n",
+    "tampered = storage.get(\"v1.0.0\")\n",
+    "tampered[\"data\"][\"entities\"][\"acme\"][\"note\"] = \"mutated after the fact\"\n",
+    "print(\"tampered:\", verify_checksum(tampered))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bd14c3e4",
+   "metadata": {},
+   "source": [
+    "## 5) Retiring a version\n",
+    "\n",
+    "`delete(label)` removes a snapshot; tags pointing at it are your responsibility to update."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "de9fe3e5",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:46:39.349814Z",
+     "iopub.status.busy": "2026-08-26T18:46:39.349513Z",
+     "iopub.status.idle": "2026-08-26T18:46:39.354710Z",
+     "shell.execute_reply": "2026-08-26T18:46:39.353669Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "False"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "storage.delete(\"v1.0.0\")\n",
+    "storage.exists(\"v1.0.0\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ab667b32",
+   "metadata": {},
+   "source": [
+    "## Summary\n",
+    "\n",
+    "| Task | API |\n",
+    "|---|---|\n",
+    "| Record audit metadata | `ChangeLogEntry(timestamp, author=email, description)` |\n",
+    "| Persist a version | `InMemoryVersionStorage().save({\"label\": ..., ...})` |\n",
+    "| Pin a release name | `save_tag(\"release\", \"v1.0.0\")` / `get_tag(\"release\")` |\n",
+    "| Integrity check | `compute_checksum(snap)` / `verify_checksum(snap)` |\n",
+    "| Persistent backend | `SQLiteVersionStorage(path)` — same interface |\n",
+    "\n",
+    "See also `semantica/change_management/change_management_usage.md` for the manager classes (`TemporalVersionManager`, `OntologyVersionManager`)."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

cookbook/introduction/25_Seed_Data.ipynb

@@ -0,0 +1,314 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6eb4dfba",
+   "metadata": {},
+   "source": [
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/semantica-agi/semantica/blob/main/cookbook/introduction/25_Seed_Data.ipynb)\n",
+    "\n",
+    "# Seed Data — Practical Guide\n",
+    "\n",
+    "The `seed` module bootstraps a knowledge graph from **trusted, pre-known data** (CSV/JSON/database/API sources) before any extraction runs. This gives extraction a foundation to link against instead of starting from an empty graph.\n",
+    "\n",
+    "Key pieces:\n",
+    "\n",
+    "- **`SeedDataManager`** — registers data sources and builds foundation graphs\n",
+    "- **`create_foundation_graph()`** — turns registered sources into `entities` + `relationships` + `metadata`\n",
+    "- **`validate_quality()`** — checks a foundation graph before you commit it\n",
+    "\n",
+    "All examples below were executed against `semantica/seed/seed_manager.py`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "32f80cc6",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:51:18.716466Z",
+     "iopub.status.busy": "2026-08-26T18:51:18.716264Z",
+     "iopub.status.idle": "2026-08-26T18:51:20.533828Z",
+     "shell.execute_reply": "2026-08-26T18:51:20.531402Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!pip install -q semantica"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "75136e5f",
+   "metadata": {},
+   "source": [
+    "## 1) Prepare a seed CSV and register the source\n",
+    "\n",
+    "`register_source(name, format, location, entity_type=...)` records where trusted data lives. `verified=True` (the default) marks the source as pre-validated."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "a8089e1f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:51:20.538772Z",
+     "iopub.status.busy": "2026-08-26T18:51:20.538323Z",
+     "iopub.status.idle": "2026-08-26T18:51:20.675403Z",
+     "shell.execute_reply": "2026-08-26T18:51:20.674060Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import csv\n",
+    "import tempfile\n",
+    "from pathlib import Path\n",
+    "from semantica.seed import SeedDataManager\n",
+    "\n",
+    "# Write the sample CSV into a session-scoped temp directory so we never\n",
+    "# clobber a companies.csv that might exist in the user's working directory.\n",
+    "seed_csv = Path(tempfile.mkdtemp(prefix=\"semantica-seed-\")) / \"companies.csv\"\n",
+    "with open(seed_csv, \"w\", newline=\"\") as f:\n",
+    "    writer = csv.DictWriter(f, fieldnames=[\"id\", \"name\", \"type\", \"industry\"])\n",
+    "    writer.writeheader()\n",
+    "    writer.writerow({\"id\": \"c1\", \"name\": \"Acme\", \"type\": \"Company\", \"industry\": \"robotics\"})\n",
+    "    writer.writerow({\"id\": \"c2\", \"name\": \"Globex\", \"type\": \"Company\", \"industry\": \"energy\"})\n",
+    "\n",
+    "manager = SeedDataManager()\n",
+    "manager.register_source(\"companies\", format=\"csv\", location=str(seed_csv), entity_type=\"Company\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e87221ba",
+   "metadata": {},
+   "source": [
+    "## 2) Load records from a registered source\n",
+    "\n",
+    "`load_source(name)` reads the source and enriches each record with `entity_type` and `source` provenance keys."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f932e550",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:51:20.679424Z",
+     "iopub.status.busy": "2026-08-26T18:51:20.679156Z",
+     "iopub.status.idle": "2026-08-26T18:51:20.690659Z",
+     "shell.execute_reply": "2026-08-26T18:51:20.688812Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div style='font-family: monospace;'><h4>🧠 Semantica - 📊 Current Progress</h4><table style='width: 100%; border-collapse: collapse;'><tr><th>Status</th><th>Action</th><th>Module</th><th>Submodule</th><th>Progress</th><th>ETA</th><th>Rate</th><th>Time</th><th>Extracted</th></tr><tr><td>✅</td><td>Semantica is seeding</td><td>🌱 seed</td><td>SeedDataManager</td><td>100.0%</td><td>-</td><td>-</td><td>0.00s</td><td>-</td></tr></table></div>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "🔄 Semantica is seeding: Loading seed data from CSV: /var/folders/7s/bvvstgs10y963tz6_4bbnklr0000gn/T/semantica-seed-eu9__ep1/companies.csv 🌱 seed SeedDataManager |░░░░░░░░░░░░░░░| 0.0% ETA: - Rate: - Time: 0.00s Extracted: -"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "loaded 2 records\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "{'id': 'c1',\n",
+       " 'name': 'Acme',\n",
+       " 'type': 'Company',\n",
+       " 'industry': 'robotics',\n",
+       " 'entity_type': 'Company',\n",
+       " 'source': 'companies'}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "records = manager.load_source(\"companies\")\n",
+    "print(f\"loaded {len(records)} records\")\n",
+    "records[0]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f2ebce64",
+   "metadata": {},
+   "source": [
+    "## 3) Build the foundation graph\n",
+    "\n",
+    "`create_foundation_graph()` converts every registered source into graph-ready entities and relationships. Entities carry `confidence: 1.0` — seed data is trusted by definition."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "09388c31",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:51:20.695259Z",
+     "iopub.status.busy": "2026-08-26T18:51:20.694928Z",
+     "iopub.status.idle": "2026-08-26T18:51:20.708595Z",
+     "shell.execute_reply": "2026-08-26T18:51:20.707072Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['entities', 'metadata', 'relationships']"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "foundation = manager.create_foundation_graph()\n",
+    "sorted(foundation.keys())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "4610a59f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:51:20.713136Z",
+     "iopub.status.busy": "2026-08-26T18:51:20.712795Z",
+     "iopub.status.idle": "2026-08-26T18:51:20.718637Z",
+     "shell.execute_reply": "2026-08-26T18:51:20.716835Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'id': 'c1',\n",
+       " 'text': 'Acme',\n",
+       " 'type': 'Company',\n",
+       " 'confidence': 1.0,\n",
+       " 'metadata': {'industry': 'robotics', 'source': 'companies'}}"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "foundation[\"entities\"][0]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f3a52dc7",
+   "metadata": {},
+   "source": [
+    "## 4) Validate quality before committing\n",
+    "\n",
+    "`validate_quality(foundation_graph)` returns `valid`, `errors`, `warnings`, and `metrics` so you can gate bad seed data before it pollutes the graph."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "4eb7e664",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-08-26T18:51:20.722674Z",
+     "iopub.status.busy": "2026-08-26T18:51:20.722118Z",
+     "iopub.status.idle": "2026-08-26T18:51:20.732003Z",
+     "shell.execute_reply": "2026-08-26T18:51:20.730170Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "quality = manager.validate_quality(foundation)\n",
+    "quality[\"valid\"]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b534be89",
+   "metadata": {},
+   "source": [
+    "## Summary\n",
+    "\n",
+    "| Task | API |\n",
+    "|---|---|\n",
+    "| Register a trusted source | `register_source(name, format, location, entity_type=...)` |\n",
+    "| Load records | `load_source(name)` — adds `entity_type` / `source` keys |\n",
+    "| Direct file load | `load_from_csv(path)` / `load_from_json(path)` |\n",
+    "| Build the graph | `create_foundation_graph()` → `entities` / `relationships` / `metadata` |\n",
+    "| Gate bad data | `validate_quality(graph)` → `valid` / `errors` / `warnings` / `metrics` |\n",
+    "\n",
+    "See also `semantica/seed/seed_usage.md` for `load_from_database`, `load_from_api`, and `integrate_with_extracted`."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/citation.md

@@ -13,33 +13,32 @@ icon: "quote-left"
   <Tab title="BibTeX">
     ```bibtex
     @software{semantica2026,
-      title   = {Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering},
-      author  = {Hawksight AI},
-      year    = {2026},
-      url     = {https://github.com/semantica-agi/semantica},
-      version = {0.6.0},
-      doi     = {10.5281/zenodo.XXXXXXX}
+      title  = {Semantica: Graph-Native Infrastructure for Context and Accountable AI Systems},
+      author = {Semantica},
+      year   = {2026},
+      url    = {https://github.com/semantica-agi/semantica},
+      doi    = {10.5281/zenodo.XXXXXXX}
     }
     ```
   </Tab>
   <Tab title="APA">
-    Hawksight AI. (2026). *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering* (Version 0.6.0) \[Computer software\]. https://github.com/semantica-agi/semantica
+    Semantica. (2026). *Semantica: Graph-Native Infrastructure for Context and Accountable AI Systems* \[Computer software\]. https://github.com/semantica-agi/semantica
   </Tab>
   <Tab title="MLA">
-    Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.6.0, GitHub, 2026, https://github.com/semantica-agi/semantica.
+    Semantica. *Semantica: Graph-Native Infrastructure for Context and Accountable AI Systems*. GitHub, 2026, https://github.com/semantica-agi/semantica.
   </Tab>
   <Tab title="Chicago">
-    Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.6.0. GitHub, 2026. https://github.com/semantica-agi/semantica.
+    Semantica. *Semantica: Graph-Native Infrastructure for Context and Accountable AI Systems*. GitHub, 2026. https://github.com/semantica-agi/semantica.
   </Tab>
   <Tab title="IEEE">
-    Hawksight AI, "Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering," Version 0.6.0, GitHub, 2026. \[Online\]. Available: https://github.com/semantica-agi/semantica
+    Semantica, "Semantica: Graph-Native Infrastructure for Context and Accountable AI Systems," GitHub, 2026. \[Online\]. Available: https://github.com/semantica-agi/semantica
   </Tab>
 </Tabs>
 
 
 ## Acknowledgment Text
 
-> "This work uses Semantica (Hawksight AI, 2026), an open-source framework for semantic layer construction and knowledge engineering."
+> "This work uses Semantica (2026), an open-source graph-native infrastructure framework for context and accountable AI systems, providing Context Graphs, knowledge graphs, and full decision provenance."
 
 
 ## Share Your Research

docs/concepts.md

@@ -16,6 +16,9 @@ At its core, Semantica adds a **context and accountability layer** on top of you
 - **Accountability Layer** — Provenance tracking, decision intelligence, conflict detection, and W3C PROV-O compliance make every claim in your AI stack auditable and explainable.
 - **Extension Layer** — `PluginRegistry` and `MethodRegistry` let you replace or augment any component: ingestors, extractors, reasoning engines, backends: without changing framework code.
 
+<Warning>
+  **This is system-level explainability, not foundation-model explainability.** Semantica does not expose, reconstruct, or explain what happens *inside* the LLM/foundation model — its internal reasoning or chain-of-thought stays opaque, as it does for any external system. What Semantica explains is *outside* the model: the context and data fed in, the decision produced, its provenance, the relevant relationships, the policies applied, and the full execution trail. In short, Semantica explains and audits *what the AI system did*, not the foundation model's private internal reasoning.
+</Warning>
 
 ## Knowledge Graphs
 

docs/cookbook.md

@@ -35,6 +35,7 @@ Essential guides to master the Semantica framework.
 - **[Vector Store](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/13_Vector_Store.ipynb)** — Setting up vector stores for similarity search and retrieval. *Intermediate*
 - **[Graph Store](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/09_Graph_Store.ipynb)** — Persisting knowledge graphs in Neo4j or FalkorDB. Topics: Neo4j, Cypher, Persistence · *Intermediate*
 - **[Ontology](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/14_Ontology.ipynb)** — Defining domain schemas and ontologies to structure your data. Topics: OWL, RDF, Schema Design · *Intermediate*
+- **[Seed Data](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/25_Seed_Data.ipynb)** — Bootstrapping a knowledge graph from trusted CSV, JSON, database, and API sources before extraction runs. Topics: SeedDataManager, Foundation Graphs · *Intermediate*
 
 
 ## Advanced Concepts
@@ -50,6 +51,9 @@ Deep dive into advanced features, customization, and complex workflows.
 - **[Multi-Source Integration](https://github.com/semantica-agi/semantica/blob/main/cookbook/advanced/06_Multi_Source_Data_Integration.ipynb)** — Merging data from disparate sources into a unified graph. Topics: Entity Resolution, Merging, Fusion · *Advanced*
 - **[Reasoning and Inference](https://github.com/semantica-agi/semantica/blob/main/cookbook/advanced/08_Reasoning_and_Inference.ipynb)** — Using logical reasoning to infer new knowledge from existing facts. Topics: Logic Rules, Inference Engines · *Advanced*
 - **[Temporal Knowledge Graphs](https://github.com/semantica-agi/semantica/blob/main/cookbook/advanced/10_Temporal_Knowledge_Graphs.ipynb)** — Modeling and querying data that changes over time. Topics: Time Series, Temporal Logic, Allen Algebra · *Advanced*
+- **[Provenance Tracking](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/22_Provenance_Tracking.ipynb)** — Audit-grade, W3C PROV-O-aligned tracking of where every entity, relationship, and chunk came from. Topics: PROV-O, Lineage, Checksums, Invalidation · *Advanced*
+- **[Reasoning Module](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/23_Reasoning.ipynb)** — Deriving new knowledge from existing facts with forward chaining, backward chaining, and Datalog strategies. Topics: Reasoner, Datalog, Explanations · *Advanced*
+- **[Change Management](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/24_Change_Management.ipynb)** — Versioning, audit trails, and data-integrity checks for knowledge graphs and ontologies. Topics: ChangeLogEntry, Version Storage, Data Integrity · *Advanced*
 
 
 ## How to Run
@@ -80,6 +84,6 @@ Deep dive into advanced features, customization, and complex workflows.
   You can also run the cookbook using Docker:
 
   ```bash
-  docker run -p 8888:8888 hawksight/semantica-cookbook
+  docker run -p 8888:8888 semantica/semantica-cookbook
   ```
 </Tip>

docs/docs.json

@@ -102,6 +102,8 @@
             "group": "Integrations",
             "pages": [
               "integrations/agno",
+              "integrations/crewai",
+              "integrations/langchain",
               "integrations/docling",
               "integrations/snowflake",
               "integrations/databricks"

docs/explorer-setup.md

@@ -162,7 +162,7 @@ semantica-explorer --graph my_graph.json --no-browser
 ```
 
 <Warning>
-  `--host 0.0.0.0` makes Explorer reachable on every network interface. The server has no built-in authentication. Only use this on a trusted private network.
+  `--host 0.0.0.0` makes Explorer reachable on every network interface. Since v0.6.5 the Explorer API requires `SEMANTICA_API_KEY` (sent as the `X-API-Key` header) and fails closed with `503` when unconfigured; unauthenticated access is only possible when `SEMANTICA_ALLOW_ANONYMOUS=true` is set explicitly. Only use this on a trusted private network.
 </Warning>
 
 

docs/faq.md

@@ -17,7 +17,7 @@ icon: "circle-question"
 | API key required? | Optional: pattern extraction works with no keys |
 | Works with LangChain / LlamaIndex? | Yes: Semantica is a layer on top, not a replacement |
 | Production-ready? | Yes: 1,000+ tests, v0.5.0 ships with 12 security fixes |
-| Latest version? | **v0.6.0** (July 2026) |
+| Latest version? | **v0.6.7** (August 2026) |
 | Local LLMs? | Yes: Ollama via LiteLLM, HuggingFaceLLM for air-gapped |
 
 
@@ -52,6 +52,16 @@ Semantica works alongside these frameworks, not against them.
 
 </Accordion>
 
+<Accordion title="Does Semantica explain an LLM's internal reasoning or chain-of-thought?" icon="triangle-exclamation">
+
+No. This is **system-level explainability, not foundation-model explainability**. Semantica does not expose, reconstruct, or explain what happens *inside* the LLM/foundation model — its internal reasoning or chain-of-thought stays opaque, as it does for any external system.
+
+What Semantica explains is *outside* the model: what context and data were used, what decision was produced, the provenance behind it, the relevant relationships, the policies applied, and the resulting decision trail.
+
+In short: Semantica explains and audits *what the AI system did* — not the foundation model's private internal reasoning.
+
+</Accordion>
+
 <Accordion title="Is Semantica free?" icon="tag">
 
 Yes: MIT licensed, no vendor lock-in, no paywalled features. Some capabilities require third-party API keys (e.g., OpenAI embeddings, Groq inference), but Semantica itself is always free and open source.

docs/getting-started.md

@@ -42,7 +42,7 @@ icon: "rocket"
       Verify installation:
       ```python
       import semantica
-      print(semantica.__version__)  # 0.6.0
+      print(semantica.__version__)  # 0.6.7
       ```
     </Check>
   </Step>

docs/governance.md

@@ -4,12 +4,12 @@ description: "Project governance model: roles, decision process, release cadence
 icon: "scale-balanced"
 ---
 
-> Semantica is maintained by Hawksight AI with community contributions under an open governance model.
+> Semantica is maintained by the Semantica team with community contributions under an open governance model.
 
 
 ## Roles
 
-- **Maintainers** — Hawksight AI team: review and merge PRs, manage releases and code quality, set project direction and community standards.
+- **Maintainers** — Semantica team: review and merge PRs, manage releases and code quality, set project direction and community standards.
 - **Contributors** — Submit code, documentation, and bug reports. Help with issues and reviews. Recognized in [CONTRIBUTORS.md](https://github.com/semantica-agi/semantica/blob/main/CONTRIBUTORS.md).
 - **Community Members** — Use Semantica, provide feedback, share use cases, and participate in GitHub Discussions and Discord.
 

docs/guides/context-graphs.md

@@ -436,6 +436,35 @@ d = graph.to_dict()
 # d["statistics"] → {"node_count": int, "edge_count": int}
 ```
 
+For a human-editable, version-control-friendly representation, save a Markdown
+directory instead:
+
+```python
+graph.save_to_file("context_graph/", format="markdown")
+
+restored = ContextGraph(advanced_analytics=True)
+restored.load_from_file("context_graph/", format="markdown")
+```
+
+The directory contains a versioned `graph.md` manifest for graph identity,
+relationships, and cross-graph link descriptors, plus one file per node under
+`nodes/`. A node's content is its Markdown body; its ID, type, properties,
+metadata, and temporal validity are YAML frontmatter. Node, edge, family, graph,
+and cross-graph link IDs are preserved across round trips.
+
+Markdown loading uses replacement semantics, like `from_dict()`: it parses and
+validates the complete directory before replacing the current graph. Invalid YAML,
+duplicate IDs, unsupported versions, and unsafe filesystem links fail without
+partially mutating the graph. As with JSON loading, an edge endpoint without a node
+file creates an `entity` stub node. Symlinks, Windows directory junctions, and other
+Windows reparse points are rejected.
+
+Re-exporting to an existing managed directory atomically replaces it, removing stale
+node files. Before replacement, Semantica validates the complete canonical export
+layout, not just the manifest header. Untracked files, assets, extra directories, or
+renamed node files therefore cause the export to fail closed instead of being deleted.
+Keep attachments and hand-written indexes outside the managed export directory.
+
 If the graph had cross-graph links created with `link_graph()`, call `resolve_links()` after loading to restore live navigation — object references cannot be serialized, so they must be reconnected manually:
 
 ```python

docs/guides/ingest.md

@@ -382,6 +382,45 @@ For authentication details (PAT vs. OAuth M2M for Databricks; password vs. key-p
 
 > **Security Note:** Never hardcode credentials (`token`, `password`, `private_key`) in production code; pass them via environment variables (e.g., `DATABRICKS_TOKEN`, `SNOWFLAKE_PASSWORD`) or a secrets manager.
 
+## Source 7 — SAP OData
+
+`SAPIngestor` ingests an Entity Set from a SAP OData service (S/4HANA Cloud, SuccessFactors, or an on-prem NetWeaver Gateway over its REST surface). It speaks OData v2 and v4, follows server-driven pagination automatically, and flattens each record into a document dict via `export_as_documents()` — the same structured "transform to text, then store" pattern as the other sources.
+
+```python
+from semantica.ingest import SAPIngestor
+
+ing = SAPIngestor(
+    base_url="https://my-sap.example.com/sap/opu/odata/sap/API_BUSINESS_PARTNER",
+    client_id="...", client_secret="...",
+    token_url="https://my-sap.example.com/oauth/token",  # OAuth2 client-credentials (BTP/S/4HANA Cloud)
+    # On-prem NetWeaver often uses Basic auth instead — swap the block above for:
+    # username="erp_user", password="...",
+)
+
+# 1. Discover an unfamiliar service: entity sets + field types from $metadata
+sets = ing.discover_service()          # [{"name": "A_BusinessPartnerSet", "fields": [...]}, ...]
+
+# 2. Pull a page-walked Entity Set (v2/v4 next links handled for you)
+partners = ing.ingest_entity_set(
+    entity_set="A_BusinessPartnerSet",
+    select="BusinessPartner,BusinessPartnerFullName",   # $select
+    top=1000,                                           # cap on total rows
+)
+
+# 3. Flatten to document dicts, then build text for the graph
+docs = ing.export_as_documents(partners)
+partner_texts = [
+    f"Business Partner {d['BusinessPartner']}: {d['BusinessPartnerFullName']}"
+    for d in docs
+]
+```
+
+- Use `expand="to_Item"` (e.g. on a sales-order header set) to pull nested line items in one request — handy for modeling order → line-item → material relationships.
+- Every outbound request, including the OAuth2 token exchange, is routed through the SSRF guard, so a user-supplied SAP URL can never reach private/loopback/link-local address space.
+- Install with `pip install 'semantica[ingest-sap]'`.
+
+> **Security Note:** Never hardcode credentials (`client_secret`, `password`) in code; pass them via environment variables (e.g., `SAP_CLIENT_SECRET`, `SAP_PASSWORD`) or a secrets manager.
+
 ## Combining All Five Sources
 
 Once you have text from each source, `AgentContext.store()` accepts a flat list of strings. Semantica embeds and indexes them together — the context graph has no concept of which string came from which source unless you add metadata explicitly.

docs/guides/pipeline.md

@@ -222,10 +222,10 @@ builder.register_step_handler("ner_extract",     run_ner)
 builder.register_step_handler("triplet_extract", run_triplets)
 builder.register_step_handler("kg_merge",        merge_into_graph)
 
-builder.add_step("ingest",   "file_ingest",     handler=ingest_stix_bundles, path="./stix_bundles/")
-builder.add_step("ner",      "ner_extract",     handler=run_ner,             confidence_threshold=0.75)
-builder.add_step("triplets", "triplet_extract", handler=run_triplets,        include_temporal=True)
-builder.add_step("store",    "kg_merge",        handler=merge_into_graph,    output_path="./cti_output/")
+builder.add_step("ingest",   "file_ingest",     path="./stix_bundles/")
+builder.add_step("ner",      "ner_extract",     confidence_threshold=0.75)
+builder.add_step("triplets", "triplet_extract", include_temporal=True)
+builder.add_step("store",    "kg_merge",        output_path="./cti_output/")
 
 # ingest feeds both ner and triplets in parallel
 builder.connect_steps("ingest",   "ner")
@@ -241,7 +241,18 @@ engine   = ExecutionEngine(max_workers=2, retry_on_failure=True)
 result   = engine.execute_pipeline(pipeline)
 ```
 
-`set_parallelism(n)` tells the engine how many steps it may run simultaneously. The topological sort guarantees that only steps whose dependencies are all completed are eligible for concurrent execution — you cannot accidentally run a step before its inputs are ready.
+`set_parallelism(n)` tells the engine how many steps it may run simultaneously; `n` must be a positive integer. The topological sort guarantees that only steps whose dependencies are all completed are eligible for concurrent execution — you cannot accidentally run a step before its inputs are ready. The effective concurrency is capped at `min(n, max_workers)`, so the engine's `max_workers` setting remains a hard resource ceiling.
+
+Concurrency is opt-in per step. A dependency layer only runs in parallel when every step in that layer is marked `parallel_safe`, the layer has more than one step, and the data flowing into the layer is a dict:
+
+```python
+builder.add_step("ner",      "ner_extract",     parallel_safe=True, confidence_threshold=0.75)
+builder.add_step("triplets", "triplet_extract", parallel_safe=True, include_temporal=True)
+```
+
+If any step in a layer is not marked `parallel_safe`, or if a step runs in delta mode, the entire layer falls back to sequential execution — parallelism never silently bypasses a step that was not declared safe. `parallel_safe` is a control field: like `dependencies`, it is consumed by the builder and never reaches your handler's config.
+
+Parallel-safe handlers must return a dict. Each step in a parallel layer receives an isolated deep copy of the layer's input, so steps cannot see each other's mutations. The per-step results are merged key by key in step declaration order: a key written by one step is added to the merged output, a key written by several steps with equal values is kept, and two steps writing different values for the same key fail the pipeline with a `ProcessingError` naming the conflicting key and both steps. Handlers that touch shared mutable resources — database connections, in-memory stores, global caches — should not be marked `parallel_safe`.
 
 ## Common Pitfalls
 

docs/guides/provenance.md

@@ -639,7 +639,7 @@ Every `ProvenanceEntry` maps directly to W3C PROV-O terms. If your compliance te
 | — | `previous_version_id` | This entry corrects/replaces a prior version of the *same* fact |
 | `prov:wasDerivedFrom` | `derived_from_id` | This entry was derived from a *different* source entity |
 | `prov:used` | `used_entities` | Entity IDs consumed to produce this one |
-| `prov:generatedAtTime` | `timestamp` | ISO datetime, auto-set to `datetime.utcnow()` at write time |
+| `prov:generatedAtTime` | `timestamp` | ISO datetime, auto-set to `utc_now_iso()` at write time |
 | `prov:qualifiedInvalidation` | `invalidated`, `invalidated_at_time`, `invalidated_by`, `invalidation_reason` | A retraction/correction recorded as a tombstone via `ProvenanceManager.invalidate()`, never a hard delete |
 | `prov:startedAtTime` / `prov:endedAtTime` | `activity_started_at_time`, `activity_ended_at_time` | Typed Activity timing — pass an `ActivityRecord` via the `activity=` kwarg to set these together with `activity_id` |
 | `prov:qualifiedGeneration`/`Generation`, `qualifiedUsage`/`Usage`, `qualifiedDerivation`/`Derivation` | (derived from the fields above) | Additive qualified forms of `wasGeneratedBy`/`used`/`wasDerivedFrom`, emitted automatically alongside the plain triples |

docs/guides/reasoning.md

@@ -150,6 +150,12 @@ HighRiskSupplier(DELTA-3)                 conf=100%  rule=Rule 3
 
 DELTA-3 is flagged even though no document described it that way — the system traced: DELTA-3 supplied GAMMA-7, and GAMMA-7 exploits critical CVEs. For rules that need priority ordering or graded confidence, use the `Rule` dataclass:
 
+If a rule has side-effecting actions, one concrete activation runs those
+actions at most once on a Reasoner instance. Re-running `forward_chain()` is
+therefore safe: already-attempted actions are not repeated. Use
+`reasoner.reset_action_history()` when you intentionally want to replay them;
+`reasoner.clear()` and `reasoner.reset()` also clear the history.
+
 ```python
 # Higher priority rules fire first; confidence propagates into InferenceResult.confidence
 reasoner.add_rule(Rule(
@@ -269,7 +275,7 @@ print("Loaded {} facts from graph".format(count))
 
 ## Step 5 — SPARQL queries over enriched working memory
 
-After forward chaining has derived new facts, `SPARQLReasoner` lets you query the enriched working memory using SPARQL triple-pattern matching with optional inference expansion:
+After forward chaining has derived new facts, `SPARQLReasoner` prepares SPARQL queries over the enriched working memory with optional inference expansion:
 
 ```python
 from semantica.reasoning import SPARQLReasoner
@@ -288,22 +294,13 @@ query = """
     }
 """
 
-# execute_query() runs: expansion → inference → deduplication
-result = sparql.execute_query(query)
-
-for binding in result.bindings:
-    print("Actor: {:15s}  CVE: {}".format(
-        binding.get("actor", "?"),
-        binding.get("cve", "?"),
-    ))
-
-# metadata shows how many results came from inference vs ground facts
-print("Original: {}  Inferred: {}".format(
-    result.metadata.get("original_count", 0),
-    result.metadata.get("inferred_count", 0),
-))
+# expand_query() applies inference rules to the query text:
+expanded = sparql.expand_query(query)
+print(expanded)
 ```
 
+`execute_query()` is not implemented yet: no triplet-store execution path exists, so it raises `NotImplementedError` rather than returning an empty result set that callers would misread as "no matches". Until execution lands, run the expanded query against your RDF store directly (for example with `rdflib`).
+
 Inspect the expanded query before running it:
 
 ```python
@@ -369,6 +366,13 @@ engine.reset()
 
 The rule network is compiled once by `build_network()`. Each subsequent `add_fact()` call propagates incrementally through only the nodes whose conditions it satisfies — not the full rule set — which keeps evaluation cost proportional to the number of new activations rather than the total rule count.
 
+With a Reasoner bound, Rete action side effects are attempted once per rule,
+bindings, and matched fact identity. Passing the same match to
+`execute_matches()` again still returns the same conclusion, but does not repeat
+its actions. Call `engine.reset_action_history()` to replay actions without
+clearing working memory. `engine.reset()` and `engine.build_network()` also
+clear the action history.
+
 ## Step 7 — Temporal interval reasoning
 
 `TemporalReasoningEngine` computes Allen interval relations between time windows, letting you identify whether two events overlap, one contains the other, they meet at a boundary, and so on across your graph:

docs/guides/shacl-validation.md

@@ -8,7 +8,7 @@ icon: "shield-check"
 
 SHACL (Shapes Constraint Language) is a standard for validating graph-based data. While an ontology defines the conceptual *schema* (the "what" exists in your domain), SHACL defines the structural *rules and constraints* (the "how" it should be structured). 
 
-In Semantica, `SHACLGenerator` produces constraint rules (shapes) based on your ontology, and `_run_pyshacl` evaluates your actual data against these rules. If a node violates a rule (e.g., missing a required property or using the wrong datatype), a detailed violation report is generated.
+In Semantica, `SHACLGenerator` produces constraint rules (shapes) based on your ontology, and the public `run_shacl_validation` function evaluates your actual data against these rules. If a node violates a rule (e.g., missing a required property or using the wrong datatype), a detailed violation report is generated. The historical `_run_pyshacl` name remains available as a compatibility alias.
 
 ## Why Use SHACL Validation?
 
@@ -55,7 +55,7 @@ Let's look at a simple, universally understood example: ensuring every `Employee
 ```python
 from semantica.context import ContextGraph
 from semantica.ontology import OntologyGenerator, SHACLGenerator, PropertyShape
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 
 # 1. Prepare your data graph
 graph = ContextGraph()
@@ -95,7 +95,7 @@ data_ttl = """
 """
 
 # 5. Run Validation
-report = _run_pyshacl(data_ttl, shacl_ttl)
+report = run_shacl_validation(data_ttl, shacl_ttl)
 
 # 6. Analyze the Report
 print(f"Graph conforms: {report.conforms}")
@@ -265,10 +265,10 @@ cve_id_shape = NodeShape(
 
 ## Step 4 — Run validation and read the report
 
-Serialize the graph to RDF, then run `_run_pyshacl` against the shapes.
+Serialize the graph to RDF, then run `run_shacl_validation` against the shapes.
 
 ```python
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 
 # Prepare your RDF data string (since export_rdf primarily exports structural metadata,
 # you typically serialize your custom data graph to Turtle using rdflib or similar).
@@ -281,7 +281,7 @@ data_ttl = """
 """
 
 # Run SHACL validation
-report = _run_pyshacl(
+report = run_shacl_validation(
     data_ttl,
     shacl_ttl,
     data_graph_format="turtle",
@@ -366,8 +366,8 @@ print(f"Malware nodes missing 'family': {len(missing_family)}")
 # e.g. graph.update_node(node_id, {"family": "UNKNOWN — requires triage"})
 
 # After remediation, re-run validation to confirm the fix
-# (re-export the patched graph to Turtle first, then call _run_pyshacl again)
-report2 = _run_pyshacl(patched_data_ttl, shacl_ttl)
+# (re-export the patched graph to Turtle first, then call run_shacl_validation again)
+report2 = run_shacl_validation(patched_data_ttl, shacl_ttl)
 print(f"Violations after remediation: {report2.violation_count}")
 # Violations after remediation: 0
 ```
@@ -377,10 +377,49 @@ print(f"Violations after remediation: {report2.violation_count}")
 ## Common Pitfalls
 
 - **Assuming the ontology automatically enforces data quality**: `SHACLGenerator` generates shapes based on what it observes in the data. If your data is missing a field, the generator won't know it was mandatory unless you explicitly inject the constraint (as shown in Step 3).
-- **Passing `ContextGraph` directly to SHACL validators**: The `_run_pyshacl` function expects an RDF string (like Turtle format), not a raw Python dictionary or `ContextGraph` object. 
+- **Passing `ContextGraph` directly to SHACL validators**: The `run_shacl_validation` function expects an RDF string (like Turtle format), not a raw Python dictionary or `ContextGraph` object.
 - **Forgetting RDF serialization**: You must serialize your graph (often via a temporary file using `export_rdf`) before validating it.
 - **Treating validation as a one-time step**: Validation should be integrated as an automated step in your CI/CD pipeline or data ingestion flow, acting as a recurring gatekeeper rather than a one-off script.
 - **Ignoring validation reports**: A graph that does not conform must be remediated. Failing to review the `violation_count` and address the issues negates the purpose of SHACL validation.
+- **Validating `sh:class`/`sh:node` range checks on a property that declares `rdfs:range` with RDFS entailment on**: RDFS is an entailment rule, not a constraint. When pyshacl runs with `inference="rdfs"`, it infers the range class onto every object of the property, so class-based constraints on that property can never fail — the report says `conforms: True` on data that does not conform:
+
+    ```python
+    from pyshacl import validate
+    from rdflib import Graph
+
+    data = Graph()
+    data.parse(
+        data="""
+        @prefix ex: <https://example.org/ns#> .
+        @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+        ex:contains rdfs:domain ex:Container ; rdfs:range ex:Item .
+        ex:box a ex:Container ; ex:contains ex:notAnItem .
+        ex:notAnItem a ex:Fish .
+        """,
+        format="turtle",
+    )
+
+    shapes = Graph()
+    shapes.parse(
+        data="""
+        @prefix ex: <https://example.org/ns#> .
+        @prefix sh: <http://www.w3.org/ns/shacl#> .
+        ex:ContainerShape a sh:NodeShape ;
+            sh:targetClass ex:Container ;
+            sh:property [ sh:path ex:contains ; sh:class ex:Item ] .
+        """,
+        format="turtle",
+    )
+
+    for inference in ("none", "rdfs"):
+        conforms, _, _ = validate(data, shacl_graph=shapes, inference=inference)
+        print(inference, conforms)
+    # none  False   <- correct: notAnItem is a Fish, not an Item
+    # rdfs  True    <- the entailment manufactured the type
+    ```
+
+    Mitigations: prefer not to declare `rdfs:range` on properties you intend to constrain with `sh:class`; when class membership is the thing under test, run validation without RDFS entailment (`inference="none"`); or express the check as a constraint the entailment cannot satisfy (for example a literal property constraint). Note the trade-off: with entailment off, `sh:targetClass` no longer reaches subclasses, so subclass hierarchies need explicit typing or inference-aware target selection. Semantica's own `run_shacl_validation` wrapper already calls pyshacl with `inference="none"`, so this pitfall only bites when calling `pyshacl.validate` directly with entailment enabled.
+- **Trusting `conforms: True` without checking the inference mode**: an inference-enabled run can hide the exact violations the shapes were written to catch (see above). Record which inference mode validation ran under alongside the result, and re-run shape sets that contain `sh:class`/`sh:node` with entailment off before treating a pass as authoritative.
 
 ---
 
@@ -396,7 +435,7 @@ A DoD CTI team enforces STIX-compatible constraints on a threat graph before sha
 from semantica.context import AgentContext, ContextGraph
 from semantica.vector_store import VectorStore
 from semantica.ontology import OntologyGenerator, SHACLGenerator, PropertyShape
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 
 graph = ContextGraph()
 ctx   = AgentContext(
@@ -448,7 +487,7 @@ data_ttl = """
 <http://example.org/hammertoss> a ex:Malware .
 """
 
-report = _run_pyshacl(data_ttl, shacl_ttl)
+report = run_shacl_validation(data_ttl, shacl_ttl)
 print(f"CTI graph conforms : {report.conforms}")
 print(f"Violations         : {report.violation_count}")
 print(f"Warnings           : {report.warning_count}")
@@ -469,7 +508,7 @@ A SOC team validates zero-trust policy nodes before publishing them to the polic
 ```python
 from semantica.context import ContextGraph
 from semantica.ontology import OntologyGenerator, SHACLGenerator, PropertyShape
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 
 graph = ContextGraph()
 graph.add_node("policy-001", "Policy", "MFA Required for Tier-1 Resources",
@@ -516,7 +555,7 @@ data_ttl = """
 <http://example.org/policy-002> a ex:Policy .
 """
 
-report = _run_pyshacl(data_ttl, shacl_ttl)
+report = run_shacl_validation(data_ttl, shacl_ttl)
 print(f"Policy graph conforms: {report.conforms}")
 # Policy graph conforms: False
 
@@ -534,7 +573,7 @@ A clinical informatics team validates trial ontology nodes before loading them i
 
 ```python
 from semantica.ontology import LLMOntologyGenerator, SHACLGenerator, PropertyShape
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 from semantica.export import export_rdf
 import tempfile, os
 
@@ -586,7 +625,7 @@ with open(tmp.name) as f:
     data_ttl = f.read()
 os.unlink(tmp.name)
 
-report = _run_pyshacl(data_ttl, shacl_ttl)
+report = run_shacl_validation(data_ttl, shacl_ttl)
 print(f"Trial data conforms: {report.conforms}")
 print(f"Warnings           : {report.warning_count}")
 ```
@@ -600,7 +639,7 @@ A credit risk team validates every `LoanApplication` node against Basel III CRE2
 ```python
 from semantica.context import ContextGraph
 from semantica.ontology import OntologyGenerator, SHACLGenerator, PropertyShape
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 
 graph = ContextGraph()
 graph.add_node("loan-001", "LoanApplication", "Prime mortgage APP-2025-88421",
@@ -645,7 +684,7 @@ data_ttl = """
     ex:ltv "0.65" .
 """
 
-report = _run_pyshacl(data_ttl, shacl_ttl)
+report = run_shacl_validation(data_ttl, shacl_ttl)
 print(f"Loan portfolio conforms: {report.conforms}")
 # Loan portfolio conforms: False
 
@@ -675,14 +714,14 @@ Call this function as a pre-publish gate; exit code 1 blocks the pipeline.
 ```python
 import sys
 from semantica.ontology import OntologyGenerator, SHACLGenerator
-from semantica.ontology.ontology_validator import _run_pyshacl
+from semantica.ontology import run_shacl_validation
 
 def validate_before_publish(data_graph_str: str, ontology: dict) -> None:
     shacl_gen   = SHACLGenerator(base_uri="https://example.org/shapes/")
     shacl_graph = shacl_gen.generate(ontology)
     shacl_ttl   = shacl_gen.serialize(shacl_graph, format="turtle")
 
-    report = _run_pyshacl(data_graph_str, shacl_ttl)
+    report = run_shacl_validation(data_graph_str, shacl_ttl)
 
     if not report.conforms:
         print(f"Graph validation FAILED — {report.violation_count} violation(s)")
@@ -700,7 +739,6 @@ def validate_before_publish(data_graph_str: str, ontology: dict) -> None:
 
 - [Ontology Management](ontology) — generate the OWL ontology that SHACL shapes are derived from
 - [Reasoning & Rules](reasoning) — complement SHACL structural constraints with logical inference rules
-- [Export & Serialization](export) — serialize graph data to Turtle/RDF/XML for `_run_pyshacl` input
+- [Export & Serialization](export) — serialize graph data to Turtle/RDF/XML for `run_shacl_validation` input
 - [Conflict Resolution](conflict-resolution) — detect and resolve data conflicts before SHACL validation
 - [Change Management](change-management) — version-gate SHACL shapes alongside ontology versions
-

docs/index.md

@@ -192,7 +192,11 @@ decision_id = context.record_decision(
 
 ## Built for Where Mistakes Have Consequences
 
-Semantica was designed for domains where every decision must be explainable and every fact must be traceable:
+Semantica was designed for domains where every decision must be explainable and every fact must be traceable.
+
+<Warning>
+  **This is system-level explainability, not foundation-model explainability.** Semantica does not expose, reconstruct, or explain what happens *inside* the LLM/foundation model — its internal reasoning or chain-of-thought stays opaque, as it does for any external system. What Semantica explains is *outside* the model: the context and data fed in, the decision produced, its provenance, the relevant relationships, the policies applied, and the full execution trail. See [Core Concepts](concepts) for the full scope note.
+</Warning>
 
 **Healthcare & Life Sciences**
 - Clinical decision support with full audit trails

docs/integrations/crewai.md

@@ -0,0 +1,147 @@
+---
+title: "CrewAI Integration"
+description: "Give CrewAI crews a shared semantic knowledge graph, decision intelligence, and graph-based retrieval via three drop-in components."
+icon: "users"
+---
+
+> Three drop-in components that bring Semantica's knowledge graph and decision intelligence into any CrewAI crew.
+
+## Installation
+
+```bash
+pip install "semantica[crewai]"
+```
+
+Requires `crewai >= 0.80.0`. If `crewai` is not installed, the integration still imports — every class carries the full Semantica API and degrades gracefully, but cannot be passed to a `Crew`.
+
+## Components at a Glance
+
+- **SemanticaKGTool** — `Agent(tools=[…])`: 5 KG construction/query actions: extract entities, extract relations, add to graph, query graph, find related.
+- **SemanticaDecisionTool** — `Agent(tools=[…])`: 5 decision intelligence actions: record decisions, find precedents, trace causal chains, analyze impact, check policies.
+- **SemanticaKnowledgeSource** — `Crew(knowledge_sources=[…])`: Serializes a `ContextGraph` into CrewAI knowledge storage so every agent gets retrieval access to the graph.
+
+## Component Details
+
+<Tabs>
+  <Tab title="SemanticaKGTool">
+    Lets agents actively **build and query** a shared `ContextGraph` mid-reasoning.
+
+    ```python
+    from crewai import Agent, Crew, Task
+    from semantica.context import ContextGraph
+    from integrations.crewai import SemanticaKGTool
+
+    graph = ContextGraph()
+
+    analyst = Agent(
+        role="Knowledge Analyst",
+        goal="Build and explore a knowledge graph from documents",
+        backstory="You map entities and relationships into a shared graph.",
+        tools=[SemanticaKGTool(graph=graph)],
+    )
+
+    crew = Crew(
+        agents=[analyst],
+        tasks=[Task(
+            description="Extract and link key entities from the brief",
+            expected_output="JSON",
+            agent=analyst,
+        )],
+    )
+    crew.kickoff()
+    ```
+
+    | Tool | Description |
+    | :------ | :------------- |
+    | `extract_entities` | Extract named entities from `text` |
+    | `extract_relations` | Extract relationships between entities in `text` |
+    | `add_to_graph` | Extract entities/relations from `text` and add them to the shared graph |
+    | `query_graph` | Keyword-search the graph by node id, type, and content using `query` |
+    | `find_related` | Find concepts related to `entity` within `hops` hops |
+
+    All actions return JSON so agents get parseable results.
+
+    **Sharing a graph:** the tool reads/writes whatever `graph` you pass in. When no `graph` is given, a fresh in-memory `ContextGraph()` is created (and a warning is logged) — two tool instances that each auto-create their own graph do **not** share knowledge. Pass the same `ContextGraph` to every agent that must share state.
+  </Tab>
+  <Tab title="SemanticaDecisionTool">
+    Exposes Semantica's decision intelligence as a native CrewAI tool, backed by `AgentContext`.
+
+    ```python
+    from crewai import Agent, Crew, Task
+    from integrations.crewai import SemanticaDecisionTool
+
+    planner = Agent(
+        role="Decision Planner",
+        goal="Make grounded, precedented decisions",
+        backstory="You record decisions and validate them against policy.",
+        tools=[SemanticaDecisionTool()],
+    )
+
+    crew = Crew(agents=[planner], tasks=[...])
+    ```
+
+    When no `AgentContext` is passed, one is created in-memory with `decision_tracking=True` and its own `ContextGraph`, so decision actions work out of the box (a warning is logged — pass the same `AgentContext` to every agent that must share decision state). Missing optional fields in `record_decision` fall back to `category="general"`, `reasoning="agent decision"`, and `outcome="recorded"`. `find_precedents` returns up to `max_precedents` results. If a knowledge graph cannot trace causality, `trace_causal_chain` returns an explicit error rather than substituting similarity-based results.
+
+    | Tool | Description |
+    | :------ | :------------- |
+    | `record_decision` | Record a decision with reasoning, outcome, and confidence |
+    | `find_precedents` | Search for similar past decisions |
+    | `trace_causal_chain` | Trace the causal chain from a decision |
+    | `analyze_impact` | Assess downstream influence of a decision |
+    | `check_policy` | Validate a proposed decision against policy rules |
+  </Tab>
+  <Tab title="SemanticaKnowledgeSource">
+    Gives **every agent in the crew** retrieval access to a `ContextGraph`.
+
+    ```python
+    from crewai import Agent, Crew, Task
+    from semantica.context import ContextGraph
+    from integrations.crewai import SemanticaKnowledgeSource
+
+    graph = ContextGraph()
+    graph.add_node(node_id="privacy", node_type="policy", content="...")
+
+    researcher = Agent(
+        role="Policy Researcher",
+        goal="Answer questions from the knowledge base",
+        backstory="You retrieve from graph knowledge to answer accurately.",
+    )
+
+    crew = Crew(
+        agents=[researcher],
+        tasks=[...],
+        knowledge_sources=[SemanticaKnowledgeSource(graph=graph)],
+    )
+    ```
+
+    On kickoff the graph's nodes and edges are serialized, chunked, and stored through CrewAI's knowledge pipeline.
+
+    > **Embedder required:** storing chunks goes through CrewAI's knowledge pipeline, which needs an embedder to be configured. Set `Crew(embedder=...)` (or provide the default credentials CrewAI falls back to, e.g. `OPENAI_API_KEY`). If no working embedder is configured, storage fails, an ERROR is logged, and agents will retrieve **nothing** — the crew still runs, but its knowledge queries return empty.
+
+    **Compatibility:** CrewAI's `BaseKnowledgeSource` contract changed between `0.80.x` and current releases (`load_content()` → `validate_content()`/`aadd()`). `SemanticaKnowledgeSource` implements both legacy and current methods, so it works across `crewai>=0.80.0`.
+  </Tab>
+</Tabs>
+
+## Checkpoints & Serialization
+
+CrewAI serializes tools and knowledge sources to JSON for checkpointing/resume. Live Semantica state (`ContextGraph`, `AgentContext`, extractors) is **excluded from that serialization** — a restored tool/source comes back with a fresh in-memory `ContextGraph` and logs a warning. Until you re-attach the live graph/context, the restored objects answer queries against an **empty** graph, so re-wire them after resuming (e.g. `restored_tool.graph = live_graph`) before agents continue.
+
+## API Reference
+
+```python
+from integrations.crewai import (
+    SemanticaKGTool,          # BaseTool: KG construction/query actions
+    SemanticaDecisionTool,    # BaseTool: decision intelligence actions
+    SemanticaKnowledgeSource, # BaseKnowledgeSource: graph → crew knowledge
+    CREWAI_AVAILABLE,         # bool: True if crewai is installed
+)
+```
+
+All three classes are usable without `crewai` installed: they carry the full Semantica API and degrade gracefully.
+
+## See Also
+
+- [Context Module](../reference/context) — AgentContext and ContextGraph backing the integration.
+- [Semantic Extraction](../reference/semantic_extract) — NERExtractor / RelationExtractor used by SemanticaKGTool.
+- [LLMs](../reference/llms) — Configure LLM providers for your crew's agents.
+- [Vector Store](../reference/vector_store) — Vector backend used by SemanticaDecisionTool.

docs/integrations/langchain.md

@@ -0,0 +1,81 @@
+---
+title: "LangChain Integration"
+description: "Drop Semantica into LangChain / LangGraph pipelines via a GraphRAG retriever, VectorStore adapter, and agent tools."
+icon: "link"
+---
+
+> Three drop-in adapters that bring Semantica's context graph and hybrid search into LangChain chains and LangGraph agents.
+
+## Installation
+
+```bash
+pip install "semantica[langchain]"
+```
+
+Requires `langchain-core >= 0.3`. If langchain-core is not installed, the integration still imports — every class carries the full Semantica API and degrades gracefully (`build()` returns `None`; branch on `LANGCHAIN_AVAILABLE`).
+
+## Components at a Glance
+
+- **SemanticaRetriever** — `BaseRetriever`: hybrid-search seeds retrieval, then graph edges are walked `hops` steps (default 2) for GraphRAG-style results.
+- **SemanticaVectorStore** — `VectorStore`: `add_texts` / `similarity_search` / `similarity_search_with_score` / `from_texts` over `HybridSearch`.
+- **SemanticaKGTool** / **SemanticaDecisionTool** — `BaseTool` subclasses: `semantica_query_graph` and `semantica_query_decisions` for LangGraph / tool-calling agents.
+
+## Component Details
+
+<Tabs>
+  <Tab title="SemanticaRetriever">
+    Hybrid search seeds retrieval; then graph edges are walked `hops` steps so results go beyond flat vector similarity. If hybrid search is omitted or fails, the retriever falls back to a `ContextGraph.query` keyword scan.
+
+    ```python
+    from integrations.langchain import SemanticaRetriever
+    from semantica.context import ContextGraph
+    from semantica.vector_store import HybridSearch
+
+    graph = ContextGraph()
+    hybrid = HybridSearch()
+
+    retriever = SemanticaRetriever(graph=graph, hybrid=hybrid, hops=2, top_k=10)
+
+    from langchain.chains import RetrievalQA
+
+    qa = RetrievalQA.from_chain_type(llm=llm, retriever=retriever)
+    ```
+  </Tab>
+  <Tab title="SemanticaVectorStore">
+    Drop-in `VectorStore` for RetrievalQA / LCEL chains. `from_texts` requires a pre-configured `hybrid` instance.
+
+    ```python
+    from integrations.langchain import SemanticaVectorStore
+
+    store = SemanticaVectorStore(hybrid=hybrid)
+    store.add_texts(
+        ["document one", "document two"],
+        metadatas=[{"source": "a"}, {"source": "b"}],
+    )
+    docs = store.similarity_search("document", k=2)
+    docs, scores = store.similarity_search_with_score("document", k=2)
+    ```
+
+    `add_texts` delegates to a Semantica vector store with `add_documents` (pass `vector_store=` to `HybridSearch` or to `SemanticaVectorStore`).
+  </Tab>
+  <Tab title="Agent tools">
+    Instances are LangChain `BaseTool`s and can be passed to an agent directly.
+    `.build()` returns the tool, or `None` when langchain-core is absent.
+
+    ```python
+    from integrations.langchain import SemanticaKGTool, SemanticaDecisionTool
+    from langgraph.prebuilt import create_react_agent
+
+    tools = [
+        SemanticaKGTool(graph),
+        SemanticaDecisionTool(graph),
+    ]
+    agent = create_react_agent(model, tools)
+    ```
+
+    | Tool | Description |
+    | :------ | :------------- |
+    | `semantica_query_graph` | Keyword / NL query over the shared context graph |
+    | `semantica_query_decisions` | Search the recorded decision log |
+  </Tab>
+</Tabs>

docs/project-license.md

@@ -12,7 +12,7 @@ icon: "file-contract"
 ```
 MIT License
 
-Copyright (c) 2026 Hawksight AI
+Copyright (c) 2026 Semantica
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/reference/context.md

@@ -435,8 +435,8 @@ print("Nodes: {}, Edges: {}".format(stats["node_count"], stats["edge_count"]))
 | `query(query, skip, limit)` | `List[Dict]` | Full-text search over node content |
 | `stats()` | `Dict` | Node/edge counts, type breakdowns, graph density |
 | `density()` | `float` | Graph density score |
-| `save_to_file(path)` | `None` | Persist graph to JSON |
-| `load_from_file(path)` | `None` | Load graph from JSON |
+| `save_to_file(path, format="json")` | `None` | Persist graph as JSON or a Markdown directory |
+| `load_from_file(path, format="json")` | `None` | Replace graph state from JSON or a Markdown directory |
 | `build_from_conversations(conversations, link_entities)` | `Dict` | Build graph from conversation data |
 | `link_graph(other_graph, source_node_id, target_node_id, link_type)` | `str` | Create cross-graph navigation link; returns `link_id` |
 | `navigate_to(link_id)` | `Tuple` | Follow a cross-graph link to `(target_graph, target_node_id)` |
@@ -625,8 +625,10 @@ malformed or duplicate fields before changing memory, and re-importing unchanged
 files is idempotent. Memory-local `entities` and `relationships` are preserved as
 provenance but are not applied to `ContextGraph` by Markdown import. Use a dedicated
 export directory: matching files are overwritten, but unrelated or stale Markdown
-files are not deleted automatically. Export refuses to overwrite symbolic links and
-uses atomic file replacement. Timestamp offsets are preserved in Markdown and
+files are not deleted automatically. Export refuses to overwrite filesystem links and
+uses atomic file replacement; import also refuses symlinks, Windows directory
+junctions, and other Windows reparse points.
+Timestamp offsets are preserved in Markdown and
 normalized to UTC only for comparisons, so aware and local-naive records can be
 queried together safely. Vector-store writes are deferred until the in-memory import
 commits; adapter synchronization remains best-effort and logs failures.

docs/reference/export.md

@@ -203,6 +203,13 @@ export_lpg(graph,  "import.cypher", method="cypher")
     exporter = SemanticNetworkYAMLExporter()
     exporter.export(graph, "graph.yaml")
     ```
+
+    The YAML exporters read `entities`/`relationships`/`triplets` (with
+    `nodes`/`edges` accepted as aliases, so `ContextGraph.to_dict()` exports
+    directly). A non-empty mapping supplying none of them raises
+    `ValidationError` rather than writing a file with every collection empty,
+    as does one whose collection value is not a list of records
+    (`{"entities": "abc"}`).
   </Tab>
   <Tab title="Graph DB Import">
     **LPGExporter** writes Cypher `CREATE` statements for Neo4j and Memgraph:
@@ -236,6 +243,12 @@ export_lpg(graph,  "import.cypher", method="cypher")
 
     Both exporters write to a file and return `None`.
 
+    `LPGExporter`, `ArangoAQLExporter`, and `Neo4jCSVExporter` resolve mapping
+    payloads on the same terms as the YAML exporters above, so an unrecognized
+    or malformed mapping is rejected instead of exported as an empty graph.
+    `Neo4jCSVExporter` still reads graph *objects* off their
+    `nodes`/`entities` and `edges`/`relationships` attributes.
+
     <Warning>
       **`ArangoAQLExporter.export()` and `LPGExporter.export()` write to a file and return `None`.** They do not return the AQL/Cypher string. Write to a file and read it back if you need the string.
     </Warning>

docs/reference/ingest.md

@@ -28,6 +28,7 @@ icon: "database"
 | `DBIngestor` | SQL databases via SQLAlchemy: tables, views, and custom queries |
 | `SnowflakeIngestor` | Snowflake data warehouse queries and table exports |
 | `DatabricksIngestor` | Databricks Unity Catalog metadata, Delta table queries, and lineage |
+| `SAPIngestor` | SAP OData services (S/4HANA Cloud, SuccessFactors, NetWeaver Gateway): entity-set discovery and ingestion with v2/v4 pagination |
 | `ParquetIngestor` | Apache Parquet files and partitioned datasets with column selection |
 | `ArrowIngestor` | Apache Arrow IPC and Feather file processing |
 | `XMLIngestor` | XXE-safe XML parsing with optional XSD schema validation |

docs/reference/provenance.md

@@ -250,7 +250,7 @@ entry = ProvenanceEntry(
     source_document="report.pdf",     # str: default ""
     source_location="Page 4",         # Optional[str]: default None
     source_quote="Relevant text...",  # Optional[str]: default None
-    timestamp="2024-01-01T12:00:00",  # str: auto-set to utcnow()
+    timestamp="2024-01-01T12:00:00+00:00",  # str: auto-set to utc_now_iso()
     first_seen=None,                  # Optional[str]: ISO timestamp
     last_updated=None,                # Optional[str]: ISO timestamp
     confidence=0.9,                   # float: default 1.0

docs/reference/reasoning.md

@@ -127,9 +127,19 @@ conclusions = reasoner.infer_facts(
 | `forward_chain()` | `List[InferenceResult]` | Derive all possible conclusions iteratively until fixpoint |
 | `backward_chain(goal, max_depth)` | `InferenceResult \| None` | Prove a specific goal string, returns `None` if unprovable |
 | `infer_facts(facts, rules)` | `List[str]` | Load facts and rules then run `forward_chain()`, returns conclusion strings |
-| `clear()` | `None` | Clear all facts and rules |
+| `reset_action_history()` | `None` | Allow actions for previously fired activations to run again |
+| `clear()` | `None` | Clear all facts, rules, and action activation history |
 | `reset()` | `None` | Alias for `clear()` |
 
+Rules with actions use at-most-once attempt semantics per concrete activation
+(rule ID, bindings, and matched facts). Calling `forward_chain()` again on the
+same instance does not repeat side effects for an activation that was already
+attempted, even when an action raised an exception. Call
+`reset_action_history()` to deliberately retry without clearing facts or rules;
+`clear()` and `reset()` also clear this history. Replacing a rule's actions in
+place does not invalidate an existing activation; reset the history explicitly
+when the replacement should be replayed.
+
 ### Rule and Fact dataclass fields
 
 ```python
@@ -230,9 +240,16 @@ engine.reset()
 | `add_fact(fact)` | `None` | Add a `Fact` to working memory and propagate through the network |
 | `match_patterns(facts)` | `List[Match]` | Match all patterns; optionally add facts before matching |
 | `execute_matches(matches)` | `List[Any]` | Execute matched rules and return their conclusion values |
-| `reset()` | `None` | Clear facts and all node activation state |
+| `reset_action_history()` | `None` | Allow actions for previously executed activations to run again |
+| `reset()` | `None` | Clear facts, node activation state, and action activation history |
 | `get_network_stats()` | `dict` | Return counts of alpha, beta, terminal nodes and facts |
 
+When a Reasoner is bound, `execute_matches()` deduplicates action side effects
+by rule ID, bindings, and matched fact identity. Re-executing a match still
+returns its conclusion for compatibility, but its actions are skipped after the
+first attempt. `reset_action_history()`, `reset()`, and `build_network()` allow
+those actions to run again.
+
 
 ## SPARQLReasoner
 

docs/reference/triplet_store.md

@@ -182,7 +182,7 @@ for row in result.bindings:
     store = TripletStore(
         backend="rdf4j",
         endpoint="http://localhost:8080/rdf4j-server",
-        repository_id="semantica",   # passed through **config
+        repository_id="semantica",   # selects the remote repository
     )
     ```
 

docs/reference/utils.md

@@ -77,7 +77,17 @@ Most users won't call utils directly: it's the **shared foundation** for all mod
     export SEMANTICA_LOG_LEVEL=DEBUG
     export SEMANTICA_LOG_FORMAT=json     # "json" | "text"
     export SEMANTICA_DISABLE_PROGRESS=true
+    export SEMANTICA_FORCE_PROGRESS=true
     ```
+
+    <Tip>
+      **Progress bars follow your terminal.** Console progress is written only when
+      stdout is an interactive terminal (or a Jupyter notebook), so piping or
+      redirecting output no longer fills logs with progress bars and escape
+      sequences. Set `SEMANTICA_DISABLE_PROGRESS` to silence progress even in a
+      terminal, or `SEMANTICA_FORCE_PROGRESS` to keep it when stdout is redirected.
+      `SEMANTICA_DISABLE_PROGRESS` wins if both are set.
+    </Tip>
   </Step>
 </Steps>
 

docs/storage-backends.md

@@ -0,0 +1,154 @@
+# Graph storage backends and feature matrix
+
+Semantica separates graph modeling from physical storage. LPG backends are accessed through `graph_store` adapters; RDF backends are accessed through `triplet_store` adapters.
+
+This page is intentionally conservative: it distinguishes between an adapter existing, a feature being generally available with that model, and a backend needing user-supplied wiring.
+
+## Status labels
+
+- `built-in`: adapter implementation exists in Semantica core.
+- `tested`: covered by automated integration fixtures or tests.
+- `example-only`: usable example exists, but support is not asserted by integration tests.
+- `interface/BYO`: interface or integration point exists; bring your own backend wiring.
+
+## Adapter inventory
+
+| Backend | Model | Adapter | Status | Reference |
+| --- | --- | --- | --- | --- |
+| Neo4j | LPG | `semantica.graph_store.Neo4jStore` | built-in | `cookbook/introduction/09_Graph_Store.ipynb` |
+| FalkorDB | LPG | `semantica.graph_store.FalkorDBStore` | built-in | `docs/reference/graph_store.md` |
+| Amazon Neptune | LPG | `semantica.graph_store.AmazonNeptuneStore` | built-in | `cookbook/introduction/21_Amazon_Neptune_Store.ipynb` |
+| Apache AGE | LPG | `semantica.graph_store.ApacheAgeStore` | built-in | `docs/graph_stores/apache_age.md` |
+| RDF4J | RDF | `semantica.triplet_store.RDF4JStore` | built-in | `cookbook/introduction/20_Triplet_Store.ipynb` |
+| Apache Jena | RDF | `semantica.triplet_store.JenaStore` | built-in | `cookbook/introduction/20_Triplet_Store.ipynb` |
+| Blazegraph | RDF | `semantica.triplet_store.BlazegraphStore` | built-in | `cookbook/introduction/20_Triplet_Store.ipynb` |
+| Anzo | RDF | `semantica.triplet_store.AnzoStore` | built-in | `cookbook/introduction/20_Triplet_Store.ipynb` |
+| Oxigraph | RDF | `semantica.triplet_store.OxigraphStore` | built-in | `docs/reference/triplet_store.md` |
+
+## Feature matrix
+
+`Yes` means the capability is expected to work with the adapter and graph model. `Partial` means the capability works with model-specific constraints. `BYO` means the user must supply or validate wiring for the backend.
+
+| Backend | Model | Ingestion | Context graph construction | Reasoning/analytics | Provenance | Known limitations |
+| --- | --- | --- | --- | --- | --- | --- |
+| Neo4j | LPG | Yes | Yes | Yes | Partial | Provenance and context metadata are stored as node and edge properties; relationship properties and stable node identifiers are required. |
+| FalkorDB | LPG | Yes | Yes | Partial | Partial | Redis-based; provenance depends on node/edge properties, and multi-graph isolation depends on the selected graph name. |
+| Amazon Neptune | LPG | Yes | Yes | Partial | Partial | Use the property-graph endpoint; AWS auth, VPC, and endpoint configuration can affect local tests. Provenance depends on node/edge properties. |
+| Apache AGE | LPG | Yes | Yes | Partial | Partial | Runs through PostgreSQL/AGE; Cypher compatibility and property handling can differ from standalone LPG engines. |
+| RDF4J | RDF | Yes | Partial | Partial | Partial | Context separation relies on named graphs; triple-level provenance may require reification or graph-level metadata. |
+| Apache Jena | RDF | Yes | Partial | Partial | Partial | Named graphs are needed for context separation; backend configuration and transaction behavior matter. |
+| Blazegraph | RDF | Yes | Partial | Partial | Partial | Use quads/named graphs for context; IRI stability and graph naming matter for provenance. |
+| Anzo | RDF | Yes | Partial | Partial | Partial | Anzo deployments are environment-specific; validate `dataset_uri`/graphmart naming, named-graph support, and provenance mapping. |
+| Oxigraph | RDF | Yes | Partial | Partial | Partial | Embedded, single-process store (in-memory or on-disk); named graphs are supported, but there is no separate server process to scale independently. |
+
+## RDF and LPG differences
+
+- LPG backends store context and provenance as graph elements and properties. If a backend does not support relationship properties, some provenance patterns may be degraded.
+- RDF backends rely on IRIs, named graphs, and optional reification. Context graphs and provenance are easiest to preserve when the store supports named graphs/quads.
+- Ingestion works across both models, but the physical representation differs: LPG stores nodes/edges directly, while RDF stores subject-predicate-object statements.
+- Reasoning and analytics should be validated against the adapter's query capabilities, especially for path traversal, property filters, and named-graph queries.
+
+## Minimal connection examples
+
+Prefer the referenced notebook cells for a working setup. The examples below show the intended adapter entrypoints, not a universal connection DSL.
+
+### Neo4j
+
+```python
+import os
+from semantica.graph_store import Neo4jStore
+
+store = Neo4jStore(
+    uri='bolt://localhost:7687',
+    user='neo4j',
+    password=os.environ['NEO4J_PASSWORD']
+)
+```
+
+### FalkorDB
+
+```python
+from semantica.graph_store import FalkorDBStore
+
+store = FalkorDBStore(
+    host='localhost',
+    port=6379,
+    graph_name='semantica'
+)
+```
+
+### Amazon Neptune
+
+```python
+from semantica.graph_store import AmazonNeptuneStore
+
+store = AmazonNeptuneStore(
+    endpoint='your-neptune-cluster-endpoint',
+    port=8182,
+    region='us-east-1'
+)
+```
+
+### Apache AGE
+
+```python
+from semantica.graph_store import ApacheAgeStore
+
+store = ApacheAgeStore(
+    connection_string='host=localhost dbname=agedb user=postgres password=postgres',
+    graph_name='semantica'
+)
+```
+
+### RDF4J
+
+```python
+from semantica.triplet_store import RDF4JStore
+
+store = RDF4JStore(
+    endpoint='http://localhost:8080/rdf4j-server',
+    repository_id='semantica'
+)
+```
+
+### Apache Jena
+
+```python
+from semantica.triplet_store import JenaStore
+
+store = JenaStore(
+    endpoint='http://localhost:3030/ds'
+)
+```
+
+### Blazegraph
+
+```python
+from semantica.triplet_store import BlazegraphStore
+
+store = BlazegraphStore(
+    endpoint='http://localhost:9999/blazegraph/sparql'
+)
+```
+
+### Anzo
+
+```python
+from semantica.triplet_store import AnzoStore
+
+store = AnzoStore(
+    endpoint='http://anzo-host:8080',
+    dataset_uri='http://cambridgesemantics.com/Graphmart/your-graphmart-id'
+)
+```
+
+### Oxigraph
+
+```python
+from semantica.triplet_store import OxigraphStore
+
+# Omit `path` for an in-memory store; pass a directory for on-disk persistence.
+store = OxigraphStore(path='./semantica-oxigraph-data')
+```
+
+Replace hostnames, ports, repositories, graphs, and credentials with values from your environment. For regulated or self-hosted deployments, keep credentials in environment variables or secret storage rather than source code.

explorer/README.md

@@ -63,7 +63,9 @@ semantica-explorer --graph my_graph.json --no-browser
 python -m semantica.explorer --graph my_graph.json
 ```
 
-> **Security note:** The Explorer API has no built-in authentication. The default `--host 127.0.0.1` binds to localhost only, so it is not reachable from other machines on your network. If you bind to `0.0.0.0`, all graph data is readable and writable by any host that can reach the port. The CLI will print a warning in that case.
+> **Security note:** Since v0.6.5 the Explorer API requires an API key on protected routes. Set the `SEMANTICA_API_KEY` environment variable and send it as the `X-API-Key` header; without a configured key, protected routes fail closed with `503` rather than serving anonymously. To opt into unauthenticated access for local development only, set `SEMANTICA_ALLOW_ANONYMOUS=true` explicitly. (`/api/health` and `/api/info` are intentionally unauthenticated.)
+>
+> The default `--host 127.0.0.1` binds to localhost only, so it is not reachable from other machines on your network. If you bind to `0.0.0.0`, all graph data is readable and writable by any host that can reach the port (subject to API-key auth). The CLI prints a warning when binding to a non-loopback host in anonymous mode or when `SEMANTICA_API_KEY` is unset.
 
 ---
 
@@ -148,6 +150,8 @@ This writes the compiled assets to `../semantica/static/`. The Python server the
 | --- | --- | --- |
 | `EXPLORER_CORS_ORIGINS` | `http://localhost:5173,http://127.0.0.1:5173` | Comma-separated list of allowed CORS origins |
 | `EXPLORER_CORS_CREDENTIALS` | `false` | Set to `true` to allow credentialed cross-origin requests (only needed behind an authenticating reverse proxy) |
+| `SEMANTICA_API_KEY` | *(unset)* | API key required on protected routes since v0.6.5; send it as the `X-API-Key` header. When unset, protected routes fail closed with `503`. |
+| `SEMANTICA_ALLOW_ANONYMOUS` | `false` | Set to `true` to opt into unauthenticated access (local development only). |
 
 ---
 
@@ -251,6 +255,11 @@ Vite automatically tries the next available port and prints the actual URL in th
 - Confirm the backend exposes the `/ws/graph-updates` WebSocket endpoint.
 - Check DevTools → Network → WS tab for the connection status and error code.
 - Ensure the backend version matches the frontend — mixing major versions can cause protocol mismatches.
+- **Authentication:** `/ws/graph-updates` enforces the same API key as the REST routes. Browsers cannot set custom headers on a WebSocket handshake, so pass the key as a query parameter instead:
+  ```
+  ws://127.0.0.1:8000/ws/graph-updates?api_key=<your-key>
+  ```
+  Non-browser clients (native apps, scripts) may send it as the `X-API-Key` header. A missing or incorrect key results in close code `4401`; if `SEMANTICA_API_KEY` is unset and `SEMANTICA_ALLOW_ANONYMOUS` is not `true`, the connection is also rejected. Note that API keys in URLs appear in server logs — prefer the header for non-browser clients.
 
 ---
 

explorer/package.json

@@ -9,7 +9,7 @@
     "lint": "eslint .",
     "preview": "vite preview",
     "test:graph-store": "node --test tests/graphStore.multi-edge.test.mjs",
-    "test:graph-workspace": "node --import tsx --test tests/graphSceneState.display.test.ts",
+    "test:graph-workspace": "node --import tsx --test tests/markdownContentViewer.test.ts tests/graphSceneState.display.test.ts tests/temporalLifecycle.test.ts",
     "test:plugin-registry": "node --import tsx --test tests/pluginRegistry.temporal.test.mjs"
   },
   "dependencies": {
@@ -29,6 +29,8 @@
     "react-arborist": "^3.4.3",
     "react-dom": "^19.2.4",
     "react-dropzone": "^15.0.0",
+    "react-markdown": "^10.1.0",
+    "remark-gfm": "^4.0.1",
     "sigma": "^3.0.2",
     "vis-data": "^8.0.3",
     "vis-timeline": "^8.5.0"

explorer/src/App.tsx

@@ -67,6 +67,14 @@ type GraphStatsPayload = {
   edges?: number;
 };
 
+type ConnectionStatus = 'checking' | 'online' | 'offline';
+
+const CONNECTION_STATUS_LABEL: Record<ConnectionStatus, string> = {
+  checking: 'Connecting…',
+  online: 'System Online',
+  offline: 'Backend Unreachable',
+};
+
 const queryClient = new QueryClient();
 
 const PREVIEW_DOTS = Array.from({ length: 42 }, (_, i) => ({
@@ -719,19 +727,34 @@ const shellStyles = `
     align-items: center;
     gap: 10px;
     margin-bottom: 24px;
+    --status-color: #4cc38a;
+    --status-shadow-a: 0 0 0 3px rgba(76, 195, 138, 0.22), 0 0 12px rgba(76, 195, 138, 0.5);
+    --status-shadow-b: 0 0 0 5px rgba(76, 195, 138, 0.1), 0 0 20px rgba(76, 195, 138, 0.35);
+  }
+
+  .landing-status-bar[data-status='checking'] {
+    --status-color: #f2b66d;
+    --status-shadow-a: 0 0 0 3px rgba(242, 182, 109, 0.22), 0 0 12px rgba(242, 182, 109, 0.5);
+    --status-shadow-b: 0 0 0 5px rgba(242, 182, 109, 0.1), 0 0 20px rgba(242, 182, 109, 0.35);
+  }
+
+  .landing-status-bar[data-status='offline'] {
+    --status-color: #ff7b72;
+    --status-shadow-a: 0 0 0 3px rgba(255, 123, 114, 0.22), 0 0 12px rgba(255, 123, 114, 0.5);
+    --status-shadow-b: 0 0 0 5px rgba(255, 123, 114, 0.1), 0 0 20px rgba(255, 123, 114, 0.35);
   }
 
   .landing-status-dot {
     width: 8px;
     height: 8px;
     border-radius: 999px;
-    background: #4cc38a;
-    box-shadow: 0 0 0 3px rgba(76, 195, 138, 0.22), 0 0 12px rgba(76, 195, 138, 0.5);
+    background: var(--status-color);
+    box-shadow: var(--status-shadow-a);
     animation: landing-pulse 2.4s ease-in-out infinite;
   }
 
   .landing-status-text {
-    color: #4cc38a;
+    color: var(--status-color);
     font: 700 11px/1 "JetBrains Mono", monospace;
     letter-spacing: 0.1em;
     text-transform: uppercase;
@@ -1323,8 +1346,8 @@ const shellStyles = `
   }
 
   @keyframes landing-pulse {
-    0%, 100% { box-shadow: 0 0 0 3px rgba(76, 195, 138, 0.22), 0 0 12px rgba(76, 195, 138, 0.5); }
-    50% { box-shadow: 0 0 0 5px rgba(76, 195, 138, 0.1), 0 0 20px rgba(76, 195, 138, 0.35); }
+    0%, 100% { box-shadow: var(--status-shadow-a); }
+    50% { box-shadow: var(--status-shadow-b); }
   }
 
   .workspace-loading {
@@ -1494,10 +1517,10 @@ function WelcomeScreen({
   onOpenDecisions: () => void;
   onOpenManage: () => void;
 }) {
-  const [stats, setStats] = useState<{ nodes: number | null; edges: number | null; ready: boolean }>({
+  const [stats, setStats] = useState<{ nodes: number | null; edges: number | null; status: ConnectionStatus }>({
     nodes: null,
     edges: null,
-    ready: false,
+    status: 'checking',
   });
 
   useEffect(() => {
@@ -1507,31 +1530,32 @@ function WelcomeScreen({
       .then((response) => (response.ok ? response.json() as Promise<GraphStatsPayload> : null))
       .then((payload) => {
         if (!payload) {
-          setStats((current) => ({ ...current, ready: false }));
+          setStats((current) => ({ ...current, status: 'offline' }));
           return;
         }
 
         setStats({
           nodes: getNumberStat(payload, ['node_count', 'nodeCount', 'nodes']),
           edges: getNumberStat(payload, ['edge_count', 'edgeCount', 'edges']),
-          ready: true,
+          status: 'online',
         });
       })
       .catch((error: unknown) => {
         if (error instanceof DOMException && error.name === 'AbortError') {
           return;
         }
-        setStats((current) => ({ ...current, ready: false }));
+        setStats((current) => ({ ...current, status: 'offline' }));
       });
 
     return () => controller.abort();
   }, []);
 
+  const isOnline = stats.status === 'online';
   const metrics: LandingMetric[] = [
     { label: 'Knowledge nodes', value: formatMetric(stats.nodes, 'Live'), tone: 'cyan' },
     { label: 'Relationships mapped', value: formatMetric(stats.edges, 'Ready'), tone: 'mint' },
     { label: 'Graph modes', value: '3', tone: 'amber' },
-    { label: stats.ready ? 'Dataset online' : 'Ready to explore', value: stats.ready ? 'Active' : 'Standby', tone: 'rose' },
+    { label: isOnline ? 'Dataset online' : 'Ready to explore', value: isOnline ? 'Active' : 'Standby', tone: 'rose' },
   ];
 
   const secondaryLaunchers: LandingAction[] = [
@@ -1574,9 +1598,9 @@ function WelcomeScreen({
         {/* ── Hero ── */}
         <section className="landing-hero">
           <div className="landing-copy">
-            <div className="landing-status-bar">
+            <div className="landing-status-bar" data-status={stats.status}>
               <div className="landing-status-dot" />
-              <span className="landing-status-text">System Online</span>
+              <span className="landing-status-text">{CONNECTION_STATUS_LABEL[stats.status]}</span>
               <div className="landing-status-divider" />
               <span className="landing-status-version">Semantica v2 · Semantic Intelligence</span>
             </div>

explorer/src/workspaces/GraphWorkspace/GraphCanvas.tsx

@@ -162,7 +162,11 @@ const SIGMA_SETTINGS = {
   hideLabelsOnMove: true,
   hideEdgesOnMove: true,
   enableEdgeEvents: true,
-  renderEdgeLabels: false,
+  // #1009: edge labels (the edge `type` — "works_for", "leads", ...) were
+  // hardcoded off, so edge text never rendered regardless of data. The
+  // labelDensity / labelGridCellSize / labelRenderedSizeThreshold settings
+  // below already throttle label density for both nodes and edges.
+  renderEdgeLabels: true,
   labelDensity: 0.7,
   labelGridCellSize: 140,
   zIndex: true,
@@ -741,6 +745,12 @@ function buildEffectAvailability(
     ? { enabled: true, available: true, reason: "Panel enabled" }
     : { enabled: false, available: false, reason: "Disabled by toggle" };
 
+  // #1009: edge labels are immediately available once the graph is loaded —
+  // they have no async analytics or zoom-tier dependency.
+  const edgeLabels = effectsState.edgeLabelsEnabled
+    ? { enabled: true, available: true, reason: "Ready" }
+    : { enabled: false, available: false, reason: "Disabled by toggle" };
+
   const diagnostics = !GRAPH_THEME.effects.diagnostics.enabledInDev
     ? { enabled: false, available: false, reason: "Disabled in production" }
     : effectsState.diagnosticsEnabled
@@ -758,6 +768,7 @@ function buildEffectAvailability(
     communities,
     centrality,
     legend,
+    edgeLabels,
     diagnostics,
   };
 }
@@ -1211,6 +1222,12 @@ function applySceneState(
       size: resolvedStyle.size,
       zIndex: resolvedStyle.zIndex,
       curvature: resolvedStyle.curvature,
+      // #1009: Sigma's edge label renderer draws data.label — the graph
+      // stores the relationship type in edgeType, which the renderer never
+      // saw, so enabling renderEdgeLabels alone left edges blank.
+      // Use || rather than ?? so that an empty-string edgeType (possible
+      // when the API returns type: "") does not produce a blank label.
+      label: resolvedStyle.hidden ? undefined : String(attrs.edgeType || data.label || ""),
     };
   });
 
@@ -1295,6 +1312,9 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle, GraphCanvasProps>(
     const onEdgeClickRef = useRef(onEdgeClick);
     const onSceneRuntimeChangeRef = useRef(onSceneRuntimeChange);
     const onCameraStateChangeRef = useRef(onCameraStateChange);
+    // #1009: tracked as a ref so the Sigma creation effect always reads the
+    // current value without needing effectsState in its dependency array.
+    const effectsStateRef = useRef(effectsState);
     const [hoveredNodeId, setHoveredNodeId] = useState<string | null>(null);
     const [zoomTier, setZoomTier] = useState<GraphZoomTier>("overview");
     const [analyticsSnapshot, setAnalyticsSnapshot] = useState<GraphAnalyticsSnapshot | null>(null);
@@ -1323,6 +1343,7 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle, GraphCanvasProps>(
     onEdgeClickRef.current = onEdgeClick;
     onSceneRuntimeChangeRef.current = onSceneRuntimeChange;
     onCameraStateChangeRef.current = onCameraStateChange;
+    effectsStateRef.current = effectsState;
 
     const behaviors = useMemo<GraphBehavior[]>(
       () => [
@@ -1835,7 +1856,13 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle, GraphCanvasProps>(
         return;
       }
 
-      const sigma = new Sigma(displayGraphRef.current, containerRef.current, SIGMA_SETTINGS);
+      const sigma = new Sigma(displayGraphRef.current, containerRef.current, {
+        ...SIGMA_SETTINGS,
+        // #1009: initialize with the current toggle value rather than the
+        // static default so that a user who disabled Edge Labels before
+        // graph/Sigma initialization sees the correct state after mount.
+        renderEdgeLabels: effectsStateRef.current.edgeLabelsEnabled,
+      });
       sigmaRef.current = sigma;
       appliedGraphVersionRef.current = graphVersionRef.current;
 
@@ -1937,6 +1964,17 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle, GraphCanvasProps>(
       });
     }, [behaviors, dispatchToBehaviors, getBehaviorContext, graphReady, syncCameraState]);
 
+    // #1009: renderEdgeLabels follows the Effects-panel toggle instead of
+    // staying hardcoded — dense graphs get their label-free edges back.
+    useEffect(() => {
+      const sigma = sigmaRef.current;
+      if (!sigma) {
+        return;
+      }
+      sigma.setSetting("renderEdgeLabels", effectsState.edgeLabelsEnabled);
+      sigma.scheduleRefresh();
+    }, [effectsState.edgeLabelsEnabled]);
+
     useEffect(() => {
       return () => {
         const sigma = sigmaRef.current;

explorer/src/workspaces/GraphWorkspace/GraphInspectorPanel.tsx

@@ -3,6 +3,7 @@ import { Loader2 } from "lucide-react";
 import { graph } from "../../store/graphStore";
 import { GRAPH_THEME, withAlpha } from "./graphTheme";
 import type { GraphSelectedNodeKind } from "./types";
+import { MarkdownContentViewer } from "./MarkdownContentViewer";
 
 export type LinkPrediction = {
   target: string;
@@ -364,6 +365,11 @@ export function GraphInspectorPanel({
     ([key]) =>
       !["x","y","valid_from","valid_until","content","source","source_url","pmid","pmids","evidence","provenance","confidence"].includes(key),
   );
+  const nodeContent = (typeof attributes?.content === "string" && attributes.content)
+    ? attributes.content
+    : (typeof properties.content === "string" && properties.content)
+    ? properties.content
+    : "";
 
   return (
     <aside style={{ padding: 24, display: "flex", flexDirection: "column", gap: 18 }}>
@@ -408,6 +414,20 @@ export function GraphInspectorPanel({
         </div>
       ) : null}
 
+      {/* Content Section — only rendered when the node carries actual content.
+           This matches the existing inspector convention: sections that have no
+           data for the current node are either hidden (temporal bounds) or closed
+           by default (Source Attribution, Properties).  Always showing an open
+           empty panel would add noise for every relationship/predicate node. */}
+      {nodeContent && (
+        <details className="node-panel-collapse" open>
+          <summary className="node-panel-summary">Content</summary>
+          <div className="node-panel-body" style={{ marginTop: 8 }}>
+            <MarkdownContentViewer content={nodeContent} />
+          </div>
+        </details>
+      )}
+
       {/* Actions */}
       <section style={sectionStyle}>
         <div style={sectionTitleStyle}>Actions</div>

explorer/src/workspaces/GraphWorkspace/GraphLoadingOverlay.tsx

@@ -1,4 +1,5 @@
 import { useEffect, useRef, useState, type CSSProperties } from "react";
+import { AlertTriangle, RefreshCw } from "lucide-react";
 
 import { GRAPH_THEME, withAlpha } from "./graphTheme";
 import { GRAPH_LOAD_STAGE_SEQUENCE, createGraphLoadProgress, getGraphLoadStageLabel } from "./graphLoading";
@@ -121,6 +122,58 @@ const LOADING_OVERLAY_CSS = `
     0% { transform: translateX(-120%); }
     100% { transform: translateX(360%); }
   }
+  .graph-stage-loader-card[data-error="true"] {
+    pointer-events: auto;
+    border-color: rgba(255, 123, 114, 0.32);
+    background:
+      radial-gradient(circle at top left, rgba(255, 123, 114, 0.12), transparent 32%),
+      linear-gradient(145deg, rgba(7, 17, 31, 0.96), rgba(24, 14, 18, 0.86));
+  }
+  .graph-stage-loader-error-mark {
+    width: 38px;
+    height: 38px;
+    flex: 0 0 auto;
+    border-radius: 12px;
+    display: grid;
+    place-items: center;
+    color: #ff9e97;
+    background: rgba(255, 123, 114, 0.12);
+    border: 1px solid rgba(255, 123, 114, 0.28);
+  }
+  .graph-stage-loader-error-detail {
+    padding: 10px 12px;
+    border-radius: 10px;
+    background: rgba(0, 0, 0, 0.32);
+    border: 1px solid rgba(255, 123, 114, 0.18);
+    color: #ffb4ae;
+    font-family: "JetBrains Mono", "Fira Code", Consolas, monospace;
+    font-size: 12px;
+    line-height: 1.55;
+    word-break: break-word;
+  }
+  .graph-stage-loader-retry {
+    display: inline-flex;
+    align-items: center;
+    gap: 7px;
+    padding: 9px 16px;
+    border-radius: 8px;
+    font-size: 13px;
+    font-weight: 700;
+    cursor: pointer;
+    border: 1px solid rgba(127, 208, 255, 0.4);
+    background: linear-gradient(135deg, rgba(74, 163, 255, 0.28), rgba(56, 210, 160, 0.16));
+    color: #e8f6ff;
+    transition: 160ms ease;
+  }
+  .graph-stage-loader-retry:hover {
+    border-color: rgba(127, 208, 255, 0.62);
+    background: linear-gradient(135deg, rgba(74, 163, 255, 0.4), rgba(56, 210, 160, 0.24));
+    transform: translateY(-1px);
+  }
+  .graph-stage-loader-retry:focus-visible {
+    outline: 2px solid #7fd0ff;
+    outline-offset: 2px;
+  }
 `;
 
 function formatLayoutSource(source: GraphLoadProgress["layoutSource"]) {
@@ -170,10 +223,14 @@ export function GraphLoadingOverlay({
   progress,
   visible,
   showGraphBehind,
+  error = null,
+  onRetry,
 }: {
   progress: GraphLoadProgress | null;
   visible: boolean;
   showGraphBehind: boolean;
+  error?: string | null;
+  onRetry?: () => void;
 }) {
   const [renderVisible, setRenderVisible] = useState(visible);
   const [exiting, setExiting] = useState(false);
@@ -226,6 +283,44 @@ export function GraphLoadingOverlay({
     return null;
   }
 
+  if (error) {
+    return (
+      <div
+        className="graph-stage-loader"
+        data-exiting={exiting}
+        style={{ background: "linear-gradient(180deg, rgba(1,4,9,0.22), rgba(1,4,9,0.5))" }}
+      >
+        <style>{LOADING_OVERLAY_CSS}</style>
+        <div className="graph-stage-loader-card" data-error="true" role="alert">
+          <div style={{ display: "flex", alignItems: "flex-start", gap: 14, marginBottom: 14 }}>
+            <div className="graph-stage-loader-error-mark" aria-hidden="true">
+              <AlertTriangle size={18} strokeWidth={2.2} />
+            </div>
+            <div style={{ minWidth: 0 }}>
+              <div style={{ color: "#ffffff", fontSize: 20, fontWeight: 700, letterSpacing: "-0.03em", marginBottom: 6 }}>
+                Could not load the graph
+              </div>
+              <div style={{ color: "#8fa8c6", fontSize: 13, lineHeight: 1.5 }}>
+                The Explorer API did not return graph data. Check that the backend is running and reachable, then try again.
+              </div>
+            </div>
+          </div>
+
+          <div className="graph-stage-loader-error-detail">{error}</div>
+
+          {onRetry ? (
+            <div style={{ display: "flex", gap: 10, marginTop: 16 }}>
+              <button type="button" className="graph-stage-loader-retry" onClick={onRetry}>
+                <RefreshCw size={14} strokeWidth={2.2} aria-hidden />
+                Retry
+              </button>
+            </div>
+          ) : null}
+        </div>
+      </div>
+    );
+  }
+
   const activeProgress = progress ?? displayProgress;
   const isLiveStage = activeProgress.phase === "stabilizing_layout" || activeProgress.showGraphBehind || showGraphBehind;
   const overlayBackground = isLiveStage

explorer/src/workspaces/GraphWorkspace/GraphRuntimeStage.tsx

@@ -1,479 +0,0 @@
-import { forwardRef, useEffect, useImperativeHandle, useMemo, useRef, useState } from "react";
-
-import { batchMergeEdges, batchMergeNodes, clearGraph, graph, type EdgeAttributes, type NodeAttributes } from "../../store/graphStore";
-import { SigmaSceneAdapter } from "./SigmaSceneAdapter";
-import { createGraphLoadProgress } from "./graphLoading";
-import { resolveDisplayGraph } from "./graphSceneState";
-import {
-  chooseColorAccessor,
-  colorForNodeKey,
-  computeDegreeMap,
-  computeEdgeSize,
-  computeNodeSize,
-  computePageRank,
-  deterministicPosition,
-} from "./graphAnalytics";
-import { GRAPH_THEME } from "./graphConfig";
-import type { GraphSceneHandle } from "./scene";
-import type {
-  GraphDataSnapshot,
-  GraphEffectsState,
-  GraphLayoutSource,
-  GraphLayoutStatus,
-  GraphLoadProgress,
-  GraphPath,
-  GraphSelectedNodeState,
-  GraphStageHandle,
-  GraphViewMode,
-} from "./types";
-
-const STAGE_EFFECTS_STATE: GraphEffectsState = {
-  pathPulseEnabled: false,
-  pathFlowEnabled: false,
-  lensEnabled: false,
-  temporalEmphasisEnabled: false,
-  semanticRegionsEnabled: false,
-  contoursEnabled: false,
-  pathfindingEnabled: false,
-  communitiesEnabled: false,
-  centralityEnabled: false,
-  legendEnabled: false,
-  diagnosticsEnabled: false,
-  lensMode: "neighborhood",
-  effectQuality: "bounded",
-};
-const EMPTY_PATH: string[] = [];
-
-const socketProtocol = () => (window.location.protocol === "https:" ? "wss:" : "ws:");
-
-function yieldToMain(): Promise<void> {
-  if ("scheduler" in window && typeof (window as Window & { scheduler?: { yield?: () => Promise<void> } }).scheduler?.yield === "function") {
-    return (window as Window & { scheduler: { yield: () => Promise<void> } }).scheduler.yield();
-  }
-  return new Promise((resolve) => setTimeout(resolve, 0));
-}
-
-function buildSelectedNodeState(nodeId: string): GraphSelectedNodeState | null {
-  if (!nodeId || !graph.hasNode(nodeId)) {
-    return null;
-  }
-
-  const attributes = graph.getNodeAttributes(nodeId) as NodeAttributes;
-  return {
-    id: nodeId,
-    label: String(attributes.label || nodeId),
-    content: String(attributes.content || attributes.label || nodeId),
-    nodeType: attributes.nodeType || "entity",
-    color: attributes.color,
-    valid_from: attributes.valid_from ?? null,
-    valid_until: attributes.valid_until ?? null,
-    properties: attributes.properties ?? {},
-    neighborCount: graph.neighbors(nodeId).length,
-    visibleNeighborCount: graph.neighbors(nodeId).length,
-    collapsedNeighborCount: 0,
-    isNeighborhoodCollapsed: false,
-    canCollapseNeighborhood: graph.neighbors(nodeId).length > 8,
-  };
-}
-
-function hasUsableCoordinate(value: unknown): value is number {
-  return typeof value === "number" && Number.isFinite(value);
-}
-
-interface GraphRuntimeStageProps {
-  snapshot: GraphDataSnapshot | null | undefined;
-  selectedNodeId: string;
-  activePath: GraphPath;
-  onNodeSelect: (nodeId: string) => void;
-  onSelectedNodeStateChange: (state: GraphSelectedNodeState | null) => void;
-  isLayoutRunning: boolean;
-  onLayoutRunningChange: (running: boolean) => void;
-  viewMode: GraphViewMode;
-  temporalTime: Date | null;
-  onActiveNodeCountChange: (count: number | null) => void;
-  onProgressChange: (progress: GraphLoadProgress | null) => void;
-  onLayoutStatusChange: (status: GraphLayoutStatus) => void;
-  onRuntimeReady: () => void;
-}
-
-export const GraphRuntimeStage = forwardRef<GraphStageHandle, GraphRuntimeStageProps>(
-  function GraphRuntimeStage(
-    {
-      snapshot,
-      selectedNodeId,
-      activePath,
-      onNodeSelect,
-      onSelectedNodeStateChange,
-      isLayoutRunning,
-      onLayoutRunningChange,
-      viewMode,
-      temporalTime,
-      onActiveNodeCountChange,
-      onProgressChange,
-      onLayoutStatusChange,
-      onRuntimeReady,
-    },
-    ref,
-  ) {
-    const sceneRef = useRef<GraphSceneHandle>(null);
-    const prevActiveIdsRef = useRef<Set<string>>(new Set());
-    const [graphVersion, setGraphVersion] = useState(0);
-    const [runtimeLayoutSource, setRuntimeLayoutSource] = useState<GraphLayoutSource>(snapshot?.summary.layoutSource ?? "runtime");
-    const displayResult = useMemo(
-      () => resolveDisplayGraph(selectedNodeId, activePath, EMPTY_PATH, viewMode, { aggregationEnabled: true }),
-      [activePath, graphVersion, selectedNodeId, viewMode],
-    );
-
-    const stageSignature = useMemo(() => (snapshot ? `${snapshot.fetchedAt}:${snapshot.summary.nodeCount}:${snapshot.summary.edgeCount}` : null), [snapshot]);
-
-    useImperativeHandle(ref, () => ({
-      fitView: () => sceneRef.current?.fitView(),
-      focusNode: (nodeId: string) => sceneRef.current?.focusNode(nodeId),
-    }), []);
-
-    useEffect(() => {
-      let cancelled = false;
-
-      async function hydrateSnapshot() {
-        if (!snapshot) {
-          return;
-        }
-
-        onProgressChange(createGraphLoadProgress({
-          phase: "computing_styling",
-          progressKind: "indeterminate",
-          nodesLoaded: snapshot.summary.nodeCount,
-          nodesTotal: snapshot.summary.nodeCount,
-          edgesLoaded: snapshot.summary.edgeCount,
-          edgesTotal: snapshot.summary.edgeCount,
-          message: "Computing runtime graph styling",
-          showGraphBehind: false,
-        }));
-
-        const degreeByNode = computeDegreeMap(snapshot.nodes, snapshot.edges);
-        const pageRankByNode = computePageRank(snapshot.nodes, snapshot.edges);
-        const nodeIndexById = new Map(snapshot.nodes.map((node, index) => [node.id, index]));
-        const previousPositions = new Map<string, { x: number; y: number }>();
-
-        graph.forEachNode((nodeId, attributes) => {
-          const raw = attributes as Partial<NodeAttributes>;
-          const x = Number(raw.x);
-          const y = Number(raw.y);
-          if (Number.isFinite(x) && Number.isFinite(y)) {
-            previousPositions.set(nodeId, { x, y });
-          }
-        });
-
-        let explicitCoordinateCount = 0;
-        let carriedCoordinateCount = 0;
-        const draftAttributes = snapshot.nodes.map((node) => {
-          const previousPosition = previousPositions.get(node.id);
-          const position = hasUsableCoordinate(node.x) && hasUsableCoordinate(node.y)
-            ? { x: node.x, y: node.y }
-            : previousPosition
-              ? previousPosition
-              : deterministicPosition(node.id, nodeIndexById.get(node.id) ?? 0, snapshot.nodes.length);
-
-          if (hasUsableCoordinate(node.x) && hasUsableCoordinate(node.y)) {
-            explicitCoordinateCount += 1;
-          } else if (previousPosition) {
-            carriedCoordinateCount += 1;
-          }
-
-          return {
-            id: node.id,
-            attributes: {
-              label: node.content || node.id,
-              x: position.x,
-              y: position.y,
-              nodeType: node.type,
-              content: node.content,
-              valid_from: node.valid_from,
-              valid_until: node.valid_until,
-              properties: node.properties,
-            } as NodeAttributes,
-          };
-        });
-
-        const layoutSource: GraphLayoutSource = explicitCoordinateCount > 0
-          ? "provided"
-          : carriedCoordinateCount > 0
-            ? "carried"
-            : "runtime";
-        const hasCoordinates = explicitCoordinateCount > 0 || carriedCoordinateCount > 0;
-        setRuntimeLayoutSource(layoutSource);
-
-        const colorAccessor = chooseColorAccessor(draftAttributes);
-        await yieldToMain();
-        if (cancelled) {
-          return;
-        }
-
-        onProgressChange(createGraphLoadProgress({
-          phase: "hydrating_scene",
-          progressKind: "indeterminate",
-          nodesLoaded: snapshot.summary.nodeCount,
-          nodesTotal: snapshot.summary.nodeCount,
-          edgesLoaded: snapshot.summary.edgeCount,
-          edgesTotal: snapshot.summary.edgeCount,
-          message: "Hydrating graph scene and renderer",
-          showGraphBehind: false,
-        }));
-
-        const nodesToMerge = draftAttributes.map(({ id, attributes }) => {
-          const colorKey = colorAccessor(id, attributes);
-          const baseColor = colorForNodeKey(colorKey);
-          const dynamicSize = computeNodeSize(id, degreeByNode, pageRankByNode);
-          return {
-            id,
-            attributes: {
-              ...attributes,
-              color: baseColor,
-              baseColor,
-              size: dynamicSize,
-              baseSize: dynamicSize,
-              degree: degreeByNode.get(id) ?? 0,
-              pageRank: pageRankByNode.get(id) ?? 0,
-              glowColor: baseColor,
-              borderColor: GRAPH_THEME.nodes.border,
-              borderSize: 1,
-            } as NodeAttributes,
-          };
-        });
-
-        const edgesToMerge = snapshot.edges.map((edge) => ({
-          id: edge.id,
-          familyId: edge.familyId,
-          source: edge.source,
-          target: edge.target,
-          attributes: {
-            edgeId: edge.id,
-            familyId: edge.familyId,
-            sourceId: edge.source,
-            targetId: edge.target,
-            weight: edge.weight,
-            edgeType: edge.type,
-            properties: edge.properties,
-            size: computeEdgeSize(edge.weight),
-            baseSize: computeEdgeSize(edge.weight),
-            color: GRAPH_THEME.edges.baseColor,
-            baseColor: GRAPH_THEME.edges.baseColor,
-          } as EdgeAttributes,
-        }));
-
-        clearGraph();
-        batchMergeNodes(nodesToMerge);
-        batchMergeEdges(edgesToMerge);
-        prevActiveIdsRef.current = new Set(snapshot.nodes.map((node) => node.id));
-
-        await yieldToMain();
-        if (cancelled) {
-          return;
-        }
-
-        onLayoutStatusChange({
-          state: layoutSource === "runtime" ? "bootstrapping" : "interactive",
-          source: layoutSource,
-          hasCoordinates,
-          layoutReady: layoutSource !== "runtime",
-          displacement: null,
-          elapsedMs: 0,
-          stableSamples: 0,
-        });
-
-        onLayoutRunningChange(layoutSource === "runtime");
-        if (selectedNodeId) {
-          sceneRef.current?.focusNode(selectedNodeId);
-        } else {
-          sceneRef.current?.getRuntime()?.requestRender();
-        }
-        setGraphVersion((current) => current + 1);
-        if (layoutSource !== "runtime") {
-          onProgressChange(null);
-        } else {
-          onProgressChange(createGraphLoadProgress({
-            phase: "stabilizing_layout",
-            progressKind: "indeterminate",
-            nodesLoaded: snapshot.summary.nodeCount,
-            nodesTotal: snapshot.summary.nodeCount,
-            edgesLoaded: snapshot.summary.edgeCount,
-            edgesTotal: snapshot.summary.edgeCount,
-            message: "Settling runtime layout",
-            showGraphBehind: true,
-            layoutSource,
-            layoutState: "bootstrapping",
-          }));
-        }
-        onRuntimeReady();
-      }
-
-      void hydrateSnapshot();
-      return () => {
-        cancelled = true;
-      };
-    }, [onLayoutRunningChange, onLayoutStatusChange, onProgressChange, onRuntimeReady, selectedNodeId, snapshot, stageSignature]);
-
-    useEffect(() => {
-      if (!selectedNodeId) {
-        onSelectedNodeStateChange(null);
-        return;
-      }
-
-      onSelectedNodeStateChange(buildSelectedNodeState(selectedNodeId));
-    }, [graphVersion, onSelectedNodeStateChange, selectedNodeId, viewMode]);
-
-    useEffect(() => {
-      if (!snapshot || !temporalTime) {
-        return;
-      }
-
-      let cancelled = false;
-
-      const applySnapshot = async () => {
-        try {
-          const response = await fetch(`/api/temporal/snapshot?at=${encodeURIComponent(temporalTime.toISOString())}`);
-          if (!response.ok || cancelled) {
-            return;
-          }
-
-          const data: { active_node_ids: string[]; active_node_count: number } = await response.json();
-          if (cancelled) {
-            return;
-          }
-
-          const nextActiveIds = new Set(data.active_node_ids);
-          requestAnimationFrame(() => {
-            if (cancelled) {
-              return;
-            }
-
-            const previous = prevActiveIdsRef.current;
-            previous.forEach((id) => {
-              if (!nextActiveIds.has(id) && graph.hasNode(id)) {
-                graph.setNodeAttribute(id, "hidden", true);
-              }
-            });
-            nextActiveIds.forEach((id) => {
-              if (graph.hasNode(id)) {
-                graph.setNodeAttribute(id, "hidden", false);
-              }
-            });
-
-            prevActiveIdsRef.current = nextActiveIds;
-            onActiveNodeCountChange(data.active_node_count);
-            sceneRef.current?.getRuntime()?.requestRender();
-          });
-        } catch (error) {
-          if (!cancelled) {
-            console.error("[GraphRuntimeStage] temporal snapshot failed", error);
-          }
-        }
-      };
-
-      void applySnapshot();
-      return () => {
-        cancelled = true;
-      };
-    }, [onActiveNodeCountChange, snapshot, temporalTime]);
-
-    useEffect(() => {
-      const socket = new WebSocket(`${socketProtocol()}//${window.location.host}/ws/graph-updates`);
-
-      socket.onmessage = (event) => {
-        try {
-          const message = JSON.parse(event.data);
-          if (message.event === "connection_ack" || message.event !== "graph_mutation") {
-            return;
-          }
-
-          const eventType = message.data?.event_type;
-          const payload = message.data?.payload;
-          if (eventType === "ADD_NODE" && payload?.id) {
-            batchMergeNodes([
-              {
-                id: payload.id,
-                attributes: {
-                  label: payload.properties?.content || payload.id,
-                  x: Number.isFinite(Number(payload.x ?? payload.properties?.x))
-                    ? Number(payload.x ?? payload.properties?.x)
-                    : deterministicPosition(payload.id, graph.order + 1, Math.max(graph.order + 1, 1)).x,
-                  y: Number.isFinite(Number(payload.y ?? payload.properties?.y))
-                    ? Number(payload.y ?? payload.properties?.y)
-                    : deterministicPosition(payload.id, graph.order + 1, Math.max(graph.order + 1, 1)).y,
-                  nodeType: payload.type,
-                  content: payload.properties?.content || payload.id,
-                  valid_from: payload.properties?.valid_from ?? null,
-                  valid_until: payload.properties?.valid_until ?? null,
-                  properties: payload.properties || {},
-                  size: 8,
-                  color: colorForNodeKey(`${payload.type || "entity"}:${payload.id}`),
-                  baseColor: colorForNodeKey(`${payload.type || "entity"}:${payload.id}`),
-                  baseSize: 8,
-                  glowColor: colorForNodeKey(`${payload.type || "entity"}:${payload.id}`),
-                  borderColor: GRAPH_THEME.nodes.border,
-                  borderSize: 1,
-                },
-              },
-            ]);
-          }
-
-          if (eventType === "ADD_EDGE" && payload?.source_id && payload?.target_id) {
-            batchMergeEdges([
-              {
-                id: String(payload.id),
-                familyId: payload.familyId ? String(payload.familyId) : String(payload.id),
-                source: payload.source_id,
-                target: payload.target_id,
-                attributes: {
-                  edgeId: String(payload.id),
-                  familyId: payload.familyId ? String(payload.familyId) : String(payload.id),
-                  sourceId: payload.source_id,
-                  targetId: payload.target_id,
-                  weight: Number(payload.weight ?? 1),
-                  edgeType: payload.type,
-                  properties: payload.properties || {},
-                  size: computeEdgeSize(Number(payload.weight ?? 1)),
-                  baseSize: computeEdgeSize(Number(payload.weight ?? 1)),
-                  color: payload.properties?.inferred ? GRAPH_THEME.edges.pathColor : GRAPH_THEME.edges.baseColor,
-                  baseColor: GRAPH_THEME.edges.baseColor,
-                },
-              },
-            ]);
-          }
-
-          sceneRef.current?.getRuntime()?.requestRender();
-          setGraphVersion((current) => current + 1);
-        } catch (error) {
-          console.error("[GraphRuntimeStage] websocket update failed", error);
-        }
-      };
-
-      return () => {
-        socket.close();
-      };
-    }, []);
-
-    return (
-      <SigmaSceneAdapter
-        ref={sceneRef}
-        onNodeSelect={onNodeSelect}
-        graphVersion={graphVersion}
-        graphReady={Boolean(snapshot)}
-        displayGraph={displayResult.graph}
-        displayMeta={displayResult.meta}
-        displayState={displayResult.state}
-        selectedEdgeId=""
-        selectedNodeId={selectedNodeId}
-        focusedNodeId={viewMode === "focused" ? selectedNodeId : ""}
-        activePath={activePath}
-        activePathEdgeIds={EMPTY_PATH}
-        effectsState={STAGE_EFFECTS_STATE}
-        isLayoutRunning={isLayoutRunning}
-        onLayoutRunningChange={onLayoutRunningChange}
-        layoutSource={runtimeLayoutSource}
-        onLayoutStatusChange={onLayoutStatusChange}
-        viewMode={viewMode}
-      />
-    );
-  },
-);

explorer/src/workspaces/GraphWorkspace/GraphWorkspace.tsx

@@ -1,4 +1,4 @@
-import { useCallback, useEffect, useMemo, useRef, useState, type ComponentType, type ReactNode } from "react";
+import { useCallback, useEffect, useId, useMemo, useRef, useState, type ComponentType, type ReactNode } from "react";
 import {
   Activity,
   Clock3,
@@ -12,6 +12,7 @@ import {
   RefreshCw,
   Search,
   Users,
+  X,
   ZoomIn,
   ZoomOut,
 } from "lucide-react";
@@ -39,6 +40,8 @@ import {
   type GraphPluginToolbarItem,
 } from "./plugins";
 import { explorationEffectsShouldLoad, neighborhoodPanelShouldLoad, temporalOverlayShouldLoad } from "./pluginRegistryPredicates";
+import { shouldFetchTemporalBounds, shouldFetchTemporalSnapshot } from "./temporalLifecyclePredicates";
+import { createTemporalSnapshotGuards, type TemporalSnapshotResponse } from "./temporalSnapshotGuards";
 import type { LinkPrediction, PathResponse } from "./GraphInspectorPanel";
 import type { GraphSceneHandle, GraphSceneRuntime } from "./scene";
 import type {
@@ -146,6 +149,7 @@ const DEFAULT_EFFECTS_STATE: GraphEffectsState = {
   communitiesEnabled: false,
   centralityEnabled: false,
   legendEnabled: false,
+  edgeLabelsEnabled: true,
   diagnosticsEnabled: false,
   lensMode: "neighborhood",
   effectQuality: "bounded",
@@ -282,37 +286,168 @@ function SegmentedModeControl({ items }: { items: GraphToolbarItem[] }) {
   );
 }
 
+const SUGGESTION_DEBOUNCE_MS = 250;
+const SUGGESTION_LIMIT = 6;
+
 function SearchCommandBar({
   value,
   disabled,
   onChange,
   onSubmit,
+  onSelectSuggestion,
 }: {
   value: string;
   disabled: boolean;
   onChange: (value: string) => void;
   onSubmit: () => void;
+  onSelectSuggestion: (result: SearchResult) => void;
 }) {
+  const [suggestions, setSuggestions] = useState<SearchResult[]>([]);
+  const [suggestionsOpen, setSuggestionsOpen] = useState(false);
+  const [highlightedIndex, setHighlightedIndex] = useState(-1);
+  const abortRef = useRef<AbortController | null>(null);
+  const debounceRef = useRef<number | null>(null);
+  const listboxId = useId();
+
+  useEffect(() => {
+    if (debounceRef.current !== null) {
+      window.clearTimeout(debounceRef.current);
+    }
+
+    const query = value.trim();
+    if (disabled || !query) {
+      abortRef.current?.abort();
+      setSuggestions([]);
+      setSuggestionsOpen(false);
+      setHighlightedIndex(-1);
+      return;
+    }
+
+    debounceRef.current = window.setTimeout(() => {
+      abortRef.current?.abort();
+      const controller = new AbortController();
+      abortRef.current = controller;
+
+      fetch("/api/graph/search", {
+        method: "POST",
+        headers: { "Content-Type": "application/json" },
+        body: JSON.stringify({ query, limit: SUGGESTION_LIMIT }),
+        signal: controller.signal,
+      })
+        .then((response) => {
+          if (!response.ok) {
+            throw new Error(`Search failed with status ${response.status}`);
+          }
+          return response.json();
+        })
+        .then((data: { results?: SearchResult[] }) => {
+          setSuggestions(data.results ?? []);
+          setSuggestionsOpen(true);
+          setHighlightedIndex(-1);
+        })
+        .catch((suggestionError: unknown) => {
+          if (suggestionError instanceof DOMException && suggestionError.name === "AbortError") {
+            return;
+          }
+          setSuggestions([]);
+          setSuggestionsOpen(false);
+          setHighlightedIndex(-1);
+        });
+    }, SUGGESTION_DEBOUNCE_MS);
+
+    return () => {
+      if (debounceRef.current !== null) {
+        window.clearTimeout(debounceRef.current);
+      }
+      abortRef.current?.abort();
+    };
+  }, [value, disabled]);
+
+  const closeSuggestions = () => {
+    setSuggestionsOpen(false);
+    setHighlightedIndex(-1);
+  };
+
+  const selectSuggestion = (result: SearchResult) => {
+    setSuggestions([]);
+    closeSuggestions();
+    onSelectSuggestion(result);
+  };
+
   return (
     <form
       className="explore-search-command"
+      role="combobox"
+      aria-expanded={suggestionsOpen && suggestions.length > 0}
+      aria-haspopup="listbox"
+      aria-owns={listboxId}
       onSubmit={(event) => {
         event.preventDefault();
-        if (!disabled) {
-          onSubmit();
+        if (disabled) return;
+        if (suggestionsOpen && highlightedIndex >= 0 && suggestions[highlightedIndex]) {
+          selectSuggestion(suggestions[highlightedIndex]);
+          return;
         }
+        closeSuggestions();
+        onSubmit();
       }}
     >
       <Search size={17} strokeWidth={2.15} aria-hidden />
       <input
         value={value}
         onChange={(event) => onChange(event.target.value)}
+        onFocus={() => {
+          if (suggestions.length > 0) {
+            setSuggestionsOpen(true);
+          }
+        }}
+        onBlur={() => {
+          window.setTimeout(closeSuggestions, 120);
+        }}
+        onKeyDown={(event) => {
+          if (!suggestionsOpen || suggestions.length === 0) return;
+          if (event.key === "ArrowDown") {
+            event.preventDefault();
+            setHighlightedIndex((current) => (current + 1) % suggestions.length);
+          } else if (event.key === "ArrowUp") {
+            event.preventDefault();
+            setHighlightedIndex((current) => (current <= 0 ? suggestions.length - 1 : current - 1));
+          } else if (event.key === "Escape") {
+            event.preventDefault();
+            closeSuggestions();
+          }
+        }}
         placeholder="Search command, node, or concept"
         aria-label="Search graph nodes"
+        aria-autocomplete="list"
+        aria-controls={listboxId}
+        aria-activedescendant={highlightedIndex >= 0 ? `${listboxId}-${highlightedIndex}` : undefined}
       />
       <button type="submit" disabled={disabled} aria-label="Search for the current query">
         Search
       </button>
+
+      {suggestionsOpen && suggestions.length > 0 ? (
+        <ul id={listboxId} role="listbox" className="explore-search-suggestions" aria-label="Search suggestions">
+          {suggestions.map((result, index) => (
+            <li
+              key={result.node.id}
+              id={`${listboxId}-${index}`}
+              role="option"
+              aria-selected={index === highlightedIndex}
+              data-highlighted={index === highlightedIndex}
+              onMouseDown={(event) => {
+                event.preventDefault();
+                selectSuggestion(result);
+              }}
+              onMouseEnter={() => setHighlightedIndex(index)}
+            >
+              <span className="explore-search-suggestion-label">{result.node.content || result.node.id}</span>
+              <span className="explore-search-suggestion-type">{result.node.type}</span>
+            </li>
+          ))}
+        </ul>
+      ) : null}
     </form>
   );
 }
@@ -577,6 +712,7 @@ const HUD_CSS = `
     gap: 10px;
   }
   .explore-search-command {
+    position: relative;
     min-width: 0;
     height: 43px;
     display: grid;
@@ -592,6 +728,50 @@ const HUD_CSS = `
     color: ${GRAPH_THEME.ui.text.muted};
     box-shadow: inset 0 1px 0 rgba(255,255,255,0.045), 0 14px 30px rgba(0,0,0,0.16);
   }
+  .explore-search-suggestions {
+    position: absolute;
+    top: calc(100% + 6px);
+    left: 0;
+    right: 0;
+    z-index: 30;
+    margin: 0;
+    padding: 6px;
+    list-style: none;
+    max-height: 288px;
+    overflow-y: auto;
+    border-radius: 14px;
+    border: 1px solid ${GRAPH_THEME.ui.control.inputBorder};
+    background: ${GRAPH_THEME.ui.surface.cardStrong};
+    box-shadow: 0 18px 40px rgba(0,0,0,0.32), inset 0 1px 0 rgba(255,255,255,0.04);
+  }
+  .explore-search-suggestions li {
+    display: flex;
+    align-items: baseline;
+    justify-content: space-between;
+    gap: 10px;
+    padding: 8px 10px;
+    border-radius: 10px;
+    cursor: pointer;
+    color: ${GRAPH_THEME.ui.text.body};
+  }
+  .explore-search-suggestions li[data-highlighted="true"] {
+    background: ${GRAPH_THEME.ui.control.hoverBg};
+  }
+  .explore-search-suggestion-label {
+    min-width: 0;
+    overflow: hidden;
+    text-overflow: ellipsis;
+    white-space: nowrap;
+    font-size: 13px;
+    font-weight: 600;
+  }
+  .explore-search-suggestion-type {
+    flex-shrink: 0;
+    font-size: 11px;
+    color: ${GRAPH_THEME.ui.text.subtle};
+    text-transform: uppercase;
+    letter-spacing: 0.04em;
+  }
   .explore-search-command:focus-within {
     border-color: ${GRAPH_THEME.ui.control.activeBorder};
     box-shadow: inset 0 1px 0 rgba(255,255,255,0.06), 0 0 0 1px ${GRAPH_THEME.ui.control.focusRing}, 0 16px 32px rgba(0,0,0,0.18);
@@ -1225,12 +1405,28 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
     }));
   }, []);
 
-  const { data: summary, isLoading, isFetching } = useLoadGraph({
+  const {
+    data: summary,
+    isLoading,
+    isFetching,
+    isError: isGraphLoadError,
+    error: graphLoadError,
+    refetch: refetchGraph,
+  } = useLoadGraph({
     enabled: true,
     onGraphReady: applyGraphReadySummary,
     onProgress: handleLoadProgress,
   });
 
+  const graphLoadErrorMessage = isGraphLoadError
+    ? (graphLoadError instanceof Error ? graphLoadError.message : "Unknown error while loading the graph.")
+    : null;
+
+  const handleRetryGraphLoad = useCallback(() => {
+    setLoadingProgress(null);
+    void refetchGraph();
+  }, [refetchGraph]);
+
   useEffect(() => {
     if (isLayoutRunning) {
       return;
@@ -1247,7 +1443,18 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
     applyGraphReadySummary(summary);
   }, [applyGraphReadySummary, graphReady, summary]);
 
+  const canFetchTemporalBounds = shouldFetchTemporalBounds(summary);
+  const canFetchTemporalSnapshot = shouldFetchTemporalSnapshot({
+    debouncedTime,
+    isLoading,
+    summary,
+  });
+
   useEffect(() => {
+    if (!canFetchTemporalBounds) {
+      return;
+    }
+
     let cancelled = false;
     const loadBounds = async () => {
       try {
@@ -1267,41 +1474,99 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
     return () => {
       cancelled = true;
     };
-  }, [summary?.nodeCount, summary?.edgeCount]);
+  }, [
+    canFetchTemporalBounds,
+    summary?.nodeCount,
+    summary?.edgeCount,
+  ]);
+
+  // Guards the snapshot lifecycle: at most one in-flight request per scrubber
+  // position (identical-`at` polls are deduplicated, breaking the idle/play
+  // polling loop), applied snapshots are cached and re-applied on revisit, and
+  // a response applies only while the scrubber is still on its position
+  // (out-of-order responses cannot clobber the active-node count).
+  const temporalSnapshotGuardsRef = useRef<ReturnType<typeof createTemporalSnapshotGuards> | null>(null);
+  if (temporalSnapshotGuardsRef.current === null) {
+    temporalSnapshotGuardsRef.current = createTemporalSnapshotGuards();
+  }
+  const temporalSnapshotGuards = temporalSnapshotGuardsRef.current;
+
+  // A new graph summary means the graph data was replaced (reload/retry);
+  // snapshots cached against the previous graph are stale, so reset all state.
+  useEffect(() => {
+    temporalSnapshotGuards.reset();
+  }, [summary]);
 
   useEffect(() => {
-    if (!debouncedTime || isLoading) return;
+    if (!canFetchTemporalSnapshot) {
+      return;
+    }
+
+    if (!debouncedTime) {
+      return;
+    }
+
+    const atMs = debouncedTime.getTime();
+    const { seq, cached } = temporalSnapshotGuards.begin(atMs);
+    if (seq === null) {
+      // An identical request is already in flight: one request per position.
+      return;
+    }
+
     let cancelled = false;
 
+    const applyData = (data: TemporalSnapshotResponse) => {
+      const nextActiveIds = new Set(data.active_node_ids);
+      requestAnimationFrame(() => {
+        if (cancelled) return;
+        if (!temporalSnapshotGuards.shouldApply(atMs, seq)) {
+          // The scrubber moved on (or this request was superseded): release the
+          // position so a return to it refetches instead of stalling.
+          temporalSnapshotGuards.finish(atMs, seq);
+          return;
+        }
+        const previous = prevActiveIdsRef.current;
+        previous.forEach((id) => {
+          if (!nextActiveIds.has(id) && graph.hasNode(id)) {
+            graph.setNodeAttribute(id, "hidden", true);
+          }
+        });
+        nextActiveIds.forEach((id) => {
+          if (graph.hasNode(id)) {
+            graph.setNodeAttribute(id, "hidden", false);
+          }
+        });
+        prevActiveIdsRef.current = nextActiveIds;
+        setActiveNodeCount(data.active_node_count);
+        setGraphVersion((current) => current + 1);
+        sceneRef.current?.getRuntime()?.requestRender();
+        temporalSnapshotGuards.apply(atMs, seq, data);
+      });
+    };
+
+    if (cached) {
+      // Returning to a position whose snapshot was already applied: re-apply
+      // the cached result without a network request.
+      applyData(cached);
+      return;
+    }
+
     const applySnapshot = async () => {
       try {
         const at = debouncedTime.toISOString();
         const response = await fetch(`/api/temporal/snapshot?at=${encodeURIComponent(at)}`);
-        if (!response.ok || cancelled) return;
-
-        const data: { active_node_ids: string[]; active_node_count: number } = await response.json();
+        if (!response.ok) {
+          // A failed request must be retryable if the scrubber returns.
+          if (!cancelled) temporalSnapshotGuards.finish(atMs, seq);
+          return;
+        }
         if (cancelled) return;
 
-        const nextActiveIds = new Set(data.active_node_ids);
-        requestAnimationFrame(() => {
-          if (cancelled) return;
-          const previous = prevActiveIdsRef.current;
-          previous.forEach((id) => {
-            if (!nextActiveIds.has(id) && graph.hasNode(id)) {
-              graph.setNodeAttribute(id, "hidden", true);
-            }
-          });
-          nextActiveIds.forEach((id) => {
-            if (graph.hasNode(id)) {
-              graph.setNodeAttribute(id, "hidden", false);
-            }
-          });
-          prevActiveIdsRef.current = nextActiveIds;
-          setActiveNodeCount(data.active_node_count);
-          setGraphVersion((current) => current + 1);
-          sceneRef.current?.getRuntime()?.requestRender();
-        });
+        const data: TemporalSnapshotResponse = await response.json();
+        if (cancelled) return;
+        applyData(data);
       } catch (fetchError) {
+        temporalSnapshotGuards.finish(atMs, seq);
         if (!cancelled) {
           console.error("[Temporal] Snapshot fetch failed", fetchError);
         }
@@ -1311,8 +1576,13 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
     applySnapshot();
     return () => {
       cancelled = true;
+      // A cancelled request must be retryable when its position is revisited.
+      temporalSnapshotGuards.finish(atMs, seq);
     };
-  }, [debouncedTime, isLoading]);
+  }, [
+    canFetchTemporalSnapshot,
+    debouncedTime,
+  ]);
 
   const resolveNodeIdForFocusedMode = useCallback((
     nodeId: string,
@@ -1523,6 +1793,11 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
     }
   }, [searchQuery]);
 
+  const handleClearSearchResults = useCallback(() => {
+    setSearchResults([]);
+    setSearchError("");
+  }, []);
+
   const handleRunPredictions = useCallback(async () => {
     if (!inspectableNodeId) return;
     setIsRunningPredictions(true);
@@ -1901,7 +2176,7 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
     viewMode,
   ]);
 
-  const showLoadingOverlay = !graphReady && (isLoading || isFetching || Boolean(loadingProgress));
+  const showLoadingOverlay = !graphReady && (isLoading || isFetching || Boolean(loadingProgress) || isGraphLoadError);
   const showSettlingStatus = graphReady && loadingProgress?.phase === "stabilizing_layout";
   const hasGraphContent = Boolean(summary?.nodeCount);
   const activePath = pathResult?.path ?? EMPTY_PATH;
@@ -2764,6 +3039,10 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
                     disabled={searchDisabled}
                     onChange={setSearchQuery}
                     onSubmit={() => void handleSearch()}
+                    onSelectSuggestion={(result) => {
+                      setSearchQuery("");
+                      focusNode(result.node.id);
+                    }}
                   />
                   <SegmentedModeControl items={viewModeItems} />
                   <div className="explore-toolbelt">
@@ -2839,20 +3118,36 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
               {searchError ? <div style={{ color: "#ff7b72", fontSize: 12 }}>{searchError}</div> : null}
 
               {searchResults.length ? (
-                <div className="explore-search-results hud-scrollbar" style={searchResultsStripStyle}>
-                  {searchResults.map((result) => (
-                    <button key={result.node.id} style={predictionCardStyle} onClick={() => focusNode(result.node.id)}>
-                      <div style={{ display: "flex", justifyContent: "space-between", gap: 12 }}>
-                        <div style={{ minWidth: 0 }}>
-                          <div style={{ color: "#fff", fontWeight: 600 }}>{result.node.content || result.node.id}</div>
-                          <div style={{ color: "#8b949e", fontSize: 12 }}>{result.node.type}</div>
-                        </div>
-                        <div style={{ color: "#58a6ff", fontSize: 12, whiteSpace: "nowrap" }}>
-                          {result.score.toFixed(3)}
-                        </div>
-                      </div>
+                <div style={{ display: "flex", flexDirection: "column", gap: 8 }}>
+                  <div style={{ display: "flex", alignItems: "center", justifyContent: "space-between", gap: 12 }}>
+                    <span style={{ color: "#8b949e", fontSize: 12 }}>
+                      {searchResults.length} result{searchResults.length === 1 ? "" : "s"}
+                    </span>
+                    <button
+                      type="button"
+                      onClick={handleClearSearchResults}
+                      style={{ ...secondaryActionButtonStyle, minHeight: 26, padding: "4px 9px", gap: 5 }}
+                      aria-label="Dismiss search results"
+                    >
+                      <X size={12} strokeWidth={2.4} />
+                      Dismiss
                     </button>
-                  ))}
+                  </div>
+                  <div className="explore-search-results hud-scrollbar" style={searchResultsStripStyle}>
+                    {searchResults.map((result) => (
+                      <button key={result.node.id} style={predictionCardStyle} onClick={() => focusNode(result.node.id)}>
+                        <div style={{ display: "flex", justifyContent: "space-between", gap: 12 }}>
+                          <div style={{ minWidth: 0 }}>
+                            <div style={{ color: "#fff", fontWeight: 600 }}>{result.node.content || result.node.id}</div>
+                            <div style={{ color: "#8b949e", fontSize: 12 }}>{result.node.type}</div>
+                          </div>
+                          <div style={{ color: "#58a6ff", fontSize: 12, whiteSpace: "nowrap" }}>
+                            {Math.round(result.score)}
+                          </div>
+                        </div>
+                      </button>
+                    ))}
+                  </div>
                 </div>
               ) : null}
 
@@ -2946,6 +3241,8 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: Grap
                     progress={loadingProgress}
                     visible={showLoadingOverlay}
                     showGraphBehind={hasGraphContent || Boolean(loadingProgress?.showGraphBehind)}
+                    error={graphLoadErrorMessage}
+                    onRetry={handleRetryGraphLoad}
                   />
                 </div>
               </div>

explorer/src/workspaces/GraphWorkspace/GraphWorkspaceShell.tsx

@@ -1,862 +0,0 @@
-import { lazy, Suspense, useCallback, useEffect, useMemo, useRef, useState, type CSSProperties } from "react";
-
-import { GraphLoadingOverlay } from "./GraphLoadingOverlay";
-import { getGraphLoadTitle } from "./graphLoading";
-import { useGraphData, useReloadGraphData } from "./useGraphData";
-import type {
-  ApiNode,
-  GraphLayoutStatus,
-  GraphLoadProgress,
-  GraphPath,
-  GraphSelectedNodeState,
-  GraphStageHandle,
-  GraphViewMode,
-} from "./types";
-
-type SearchResult = {
-  node: {
-    id: string;
-    type: string;
-    content: string;
-    properties: Record<string, unknown>;
-  };
-  score: number;
-};
-
-type LinkPrediction = {
-  target: string;
-  type: string;
-  label?: string;
-  score: number;
-};
-
-type PathResponse = {
-  path: GraphPath;
-  total_weight: number;
-  hop_count: number;
-  distance_band: "direct" | "near" | "mid-range" | "distant";
-};
-
-type TemporalBounds = {
-  min?: string | null;
-  max?: string | null;
-};
-
-const GraphRuntimeStage = lazy(() =>
-  import("./GraphRuntimeStage").then((module) => ({ default: module.GraphRuntimeStage })),
-);
-const TimelinePanel = lazy(() =>
-  import("./TimelinePanel").then((module) => ({ default: module.TimelinePanel })),
-);
-
-const HUD_CSS = `
-  .palantir-bg {
-    background:
-      radial-gradient(circle at top, rgba(103, 182, 255, 0.1), transparent 24%),
-      linear-gradient(180deg, #07111d 0%, #02060e 100%);
-  }
-  .palantir-grid {
-    position: absolute;
-    inset: 0;
-    background-image:
-      linear-gradient(rgba(88, 166, 255, 0.04) 1px, transparent 1px),
-      linear-gradient(90deg, rgba(88, 166, 255, 0.04) 1px, transparent 1px);
-    background-size: 44px 44px;
-    pointer-events: none;
-    z-index: 1;
-    opacity: 0.78;
-  }
-  .palantir-vignette {
-    position: absolute;
-    inset: 0;
-    background: radial-gradient(ellipse at center, transparent 34%, rgba(1, 4, 9, 0.88) 100%);
-    pointer-events: none;
-    z-index: 2;
-  }
-  .hud-scrollbar::-webkit-scrollbar { width: 6px; }
-  .hud-scrollbar::-webkit-scrollbar-track { background: transparent; }
-  .hud-scrollbar::-webkit-scrollbar-thumb { background: rgba(88, 166, 255, 0.25); border-radius: 6px; }
-  .graph-shell-top { position: absolute; top: 18px; left: 18px; right: 18px; z-index: 10; display: flex; justify-content: space-between; align-items: flex-start; gap: 16px; pointer-events: none; }
-  .graph-status-card, .graph-command-card {
-    pointer-events: auto;
-    border: 1px solid rgba(132, 197, 255, 0.12);
-    background: linear-gradient(180deg, rgba(7, 16, 29, 0.86), rgba(10, 22, 39, 0.72)), radial-gradient(circle at top, rgba(103, 182, 255, 0.08), transparent 50%);
-    box-shadow: 0 18px 42px rgba(0, 0, 0, 0.28), inset 0 1px 0 rgba(255,255,255,0.04);
-    backdrop-filter: blur(18px);
-  }
-  .graph-status-card { width: min(420px, 38vw); border-radius: 24px; padding: 16px 18px; }
-  .graph-command-card { width: min(620px, 55vw); border-radius: 24px; padding: 14px; display: flex; flex-direction: column; gap: 12px; }
-  .graph-status-label { display: inline-flex; align-items: center; gap: 8px; color: rgba(160, 191, 223, 0.88); font-size: 11px; font-weight: 800; text-transform: uppercase; letter-spacing: 0.08em; margin-bottom: 10px; }
-  .graph-status-label::before { content: ""; width: 7px; height: 7px; border-radius: 999px; background: linear-gradient(135deg, #8ed3ff, #ffb36a); box-shadow: 0 0 12px rgba(142, 211, 255, 0.5); }
-  .graph-status-title { color: #eef5ff; font-size: 20px; font-weight: 800; letter-spacing: -0.04em; margin-bottom: 6px; }
-  .graph-status-copy { color: #8fa8c6; font-size: 12px; line-height: 1.55; margin-bottom: 14px; max-width: 40ch; }
-  .graph-status-metrics, .graph-command-row, .graph-toggle-cluster, .graph-action-cluster { display: flex; gap: 8px; flex-wrap: wrap; }
-  .graph-command-row { justify-content: space-between; align-items: center; gap: 10px; }
-  .graph-search-shell { flex: 1; min-width: 260px; display: flex; align-items: center; gap: 10px; padding: 8px 10px 8px 14px; border-radius: 18px; border: 1px solid rgba(132, 197, 255, 0.12); background: rgba(0, 0, 0, 0.18); box-shadow: inset 0 1px 0 rgba(255,255,255,0.03); }
-  .graph-search-shell input { flex: 1; min-width: 0; border: none !important; background: transparent !important; padding: 0 !important; margin: 0 !important; }
-  .graph-search-shell input:focus { outline: none; }
-  .graph-search-results { position: absolute; top: 120px; right: 18px; width: min(420px, calc(100vw - 132px)); max-height: 320px; overflow-y: auto; padding: 12px; border-radius: 20px; border: 1px solid rgba(132, 197, 255, 0.14); background: linear-gradient(180deg, rgba(8, 18, 33, 0.94), rgba(10, 21, 38, 0.86)); box-shadow: 0 18px 50px rgba(0,0,0,0.34); backdrop-filter: blur(18px); pointer-events: auto; z-index: 11; }
-  .graph-search-results-label { color: #6f89ab; font-size: 11px; font-weight: 700; text-transform: uppercase; letter-spacing: 0.08em; margin-bottom: 10px; }
-  .graph-search-result-card { width: 100%; text-align: left; padding: 12px 14px; border-radius: 16px; border: 1px solid rgba(132, 197, 255, 0.08); background: rgba(255, 255, 255, 0.025); cursor: pointer; transition: transform 160ms ease, border-color 160ms ease, background 160ms ease; }
-  .graph-search-result-card:hover { transform: translateY(-1px); border-color: rgba(132, 197, 255, 0.18); background: rgba(103, 182, 255, 0.08); }
-  .graph-inspector { pointer-events: auto; position: absolute; right: 18px; top: 154px; bottom: 108px; width: 380px; overflow-y: auto; transition: transform 0.34s cubic-bezier(0.16,1,0.3,1), opacity 0.22s ease; border-radius: 28px; border: 1px solid rgba(132, 197, 255, 0.14); background: linear-gradient(180deg, rgba(8, 18, 33, 0.9), rgba(6, 12, 22, 0.88)), radial-gradient(circle at top, rgba(103, 182, 255, 0.08), transparent 40%); box-shadow: -18px 0 48px rgba(0, 0, 0, 0.32), inset 0 1px 0 rgba(255,255,255,0.04); backdrop-filter: blur(20px); }
-  .graph-inspector[data-open='false'] { transform: translateX(calc(100% + 24px)); opacity: 0; }
-  @keyframes sem-loader-pulse {
-    0%, 100% { transform: translateY(0) scale(0.92); opacity: 0.55; }
-    50% { transform: translateY(-4px) scale(1.08); opacity: 1; }
-  }
-  @media (max-width: 1220px) {
-    .graph-shell-top { flex-direction: column; align-items: stretch; }
-    .graph-status-card, .graph-command-card { width: auto; }
-    .graph-search-results { top: 202px; right: 18px; left: 18px; width: auto; }
-  }
-`;
-
-function useDebounce<T>(value: T, delay: number): T {
-  const [debouncedValue, setDebouncedValue] = useState<T>(value);
-  useEffect(() => {
-    const timeout = setTimeout(() => setDebouncedValue(value), delay);
-    return () => clearTimeout(timeout);
-  }, [delay, value]);
-  return debouncedValue;
-}
-
-function sourceAttribution(properties: Record<string, unknown>) {
-  const keys = ["source", "source_url", "pmid", "pmids", "evidence", "provenance", "confidence"];
-  return keys
-    .filter((key) => key in properties)
-    .map((key) => ({ key, value: properties[key] }));
-}
-
-function toSelectedNodeState(node: ApiNode, neighborCount: number, fallbackColor = "#58a6ff"): GraphSelectedNodeState {
-  return {
-    id: node.id,
-    label: node.content || node.id,
-    content: node.content || node.id,
-    nodeType: node.type,
-    color: fallbackColor,
-    valid_from: node.valid_from ?? null,
-    valid_until: node.valid_until ?? null,
-    properties: node.properties ?? {},
-    neighborCount,
-    visibleNeighborCount: neighborCount,
-    collapsedNeighborCount: 0,
-    isNeighborhoodCollapsed: false,
-    canCollapseNeighborhood: neighborCount > 8,
-  };
-}
-
-function TimelineFallback({ min, max }: TemporalBounds) {
-  return (
-    <div
-      style={{
-        width: "100%",
-        height: "90px",
-        borderTop: "1px solid rgba(88, 166, 255, 0.2)",
-        background: "rgba(1, 4, 9, 0.88)",
-        display: "flex",
-        alignItems: "center",
-        justifyContent: "space-between",
-        padding: "0 18px",
-        color: "#8fa8c6",
-        fontSize: 12,
-        flexShrink: 0,
-      }}
-    >
-      <span>Temporal scrubber</span>
-      <span>{min || max ? "Preparing timeline runtime..." : "Temporal bounds loading..."}</span>
-    </div>
-  );
-}
-
-function NodePanel({
-  node,
-  predictions,
-  predictionType,
-  onPredictionTypeChange,
-  onRunPredictions,
-  pathTargetId,
-  onPathTargetChange,
-  onTracePath,
-  pathResult,
-  onDownloadProvenance,
-}: {
-  node: GraphSelectedNodeState | null;
-  predictions: LinkPrediction[];
-  predictionType: string;
-  onPredictionTypeChange: (value: string) => void;
-  onRunPredictions: () => void;
-  pathTargetId: string;
-  onPathTargetChange: (value: string) => void;
-  onTracePath: () => void;
-  pathResult: PathResponse | null;
-  onDownloadProvenance: (format: "json" | "markdown") => void;
-}) {
-  if (!node) {
-    return (
-      <div style={{ padding: 32, textAlign: "center" }}>
-        <p style={{ color: "#8b949e", fontSize: 14, margin: 0 }}>
-          Search for a node or click one in the canvas to inspect its properties.
-        </p>
-      </div>
-    );
-  }
-
-  const properties = node.properties ?? {};
-  const attribution = sourceAttribution(properties);
-  const accentColor = node.color || "#58a6ff";
-  const propertyEntries = Object.entries(properties).filter(([key]) => !["x", "y", "valid_from", "valid_until", "content", "source", "source_url", "pmid", "pmids", "evidence", "provenance", "confidence"].includes(key));
-
-  return (
-    <aside style={{ padding: 24, display: "flex", flexDirection: "column", gap: 18 }}>
-      <div style={{ borderBottom: "1px solid rgba(88, 166, 255, 0.14)", paddingBottom: 16 }}>
-        <div style={{ display: "flex", alignItems: "center", gap: 10, marginBottom: 8 }}>
-          <span style={{ background: accentColor, boxShadow: `0 0 10px ${accentColor}`, width: 8, height: 8, borderRadius: "50%" }} />
-          <span style={{ color: accentColor, fontSize: 12, fontWeight: 800, textTransform: "uppercase", letterSpacing: "0.08em" }}>{node.nodeType || "Entity"}</span>
-        </div>
-        <h3 style={{ margin: 0, color: "#fff", fontSize: 24, lineHeight: 1, fontWeight: 800, letterSpacing: "-0.04em", wordBreak: "break-word" }}>{node.label}</h3>
-        <div style={{ color: "#8b949e", fontSize: 12, marginTop: 8 }}>{node.id}</div>
-        <div style={{ display: "flex", gap: 8, flexWrap: "wrap", marginTop: 12 }}>
-          {node.valid_from || node.valid_until ? <span style={subtleChipStyle}>temporal</span> : null}
-          <span style={subtleChipStyle}>{node.neighborCount} neighbors</span>
-          {attribution.length ? <span style={subtleChipStyle}>{attribution.length} source fields</span> : null}
-          {predictions.length ? <span style={subtleChipStyle}>{predictions.length} candidate links</span> : null}
-        </div>
-      </div>
-
-      <section style={sectionStyle}>
-        <div style={sectionTitleStyle}>Actions</div>
-        <div style={{ display: "flex", flexDirection: "column", gap: 10 }}>
-          <button style={{ ...actionButtonStyle, width: "100%", justifyContent: "center" }} onClick={onRunPredictions}>Run Link Prediction</button>
-          <div style={{ display: "flex", gap: 8, flexWrap: "wrap" }}>
-            <button style={secondaryActionButtonStyle} onClick={() => onDownloadProvenance("json")}>Provenance JSON</button>
-            <button style={secondaryActionButtonStyle} onClick={() => onDownloadProvenance("markdown")}>Provenance MD</button>
-          </div>
-        </div>
-        <input value={predictionType} onChange={(event) => onPredictionTypeChange(event.target.value)} placeholder="Optional candidate type filter, e.g. disease" style={inputStyle} />
-      </section>
-
-      <section style={sectionStyle}>
-        <div style={sectionTitleStyle}>Trace Path</div>
-        <input value={pathTargetId} onChange={(event) => onPathTargetChange(event.target.value)} placeholder="Target node ID" style={inputStyle} />
-        <button style={actionButtonStyle} onClick={onTracePath}>Trace Causal Path</button>
-        {pathResult?.path?.length ? (
-          <div style={{ display: "flex", flexDirection: "column", gap: 6, marginTop: 10 }}>
-            {pathResult.path.map((step, index) => (
-              <div key={`${step}-${index}`} style={pathStepStyle}>{index + 1}. {step}</div>
-            ))}
-            <div style={{ color: "#79c0ff", fontSize: 12, marginTop: 4 }}>total weight: {pathResult.total_weight.toFixed(3)}</div>
-          </div>
-        ) : (
-          <div style={emptyTextStyle}>Choose a target or click a candidate prediction to prepare a path trace.</div>
-        )}
-      </section>
-
-      <details style={collapseStyle} open={predictions.length > 0}>
-        <summary style={summaryStyle}>Candidate Links</summary>
-        <div style={{ padding: "0 14px 14px" }}>
-          {predictions.length > 0 ? (
-            <div style={{ display: "flex", flexDirection: "column", gap: 8 }}>
-              {predictions.map((prediction) => (
-                <button key={`${prediction.target}-${prediction.type}`} style={predictionCardStyle} onClick={() => onPathTargetChange(prediction.target)}>
-                  <div style={{ color: "#fff", fontWeight: 600 }}>{prediction.label || prediction.target}</div>
-                  <div style={{ color: "#8b949e", fontSize: 12 }}>{prediction.type}</div>
-                  <div style={{ color: "#58a6ff", fontSize: 12, marginTop: 4 }}>confidence {prediction.score.toFixed(3)}</div>
-                </button>
-              ))}
-            </div>
-          ) : (
-            <div style={emptyTextStyle}>Run link prediction to surface likely next-hop relationships.</div>
-          )}
-        </div>
-      </details>
-
-      <details style={collapseStyle}>
-        <summary style={summaryStyle}>Source Attribution</summary>
-        <div style={{ padding: "0 14px 14px" }}>
-          {attribution.length ? (
-            <div style={{ display: "flex", flexDirection: "column", gap: 8 }}>
-              {attribution.map(({ key, value }) => (
-                <div key={key} style={propertyCardStyle}>
-                  <div style={{ color: "rgba(88, 166, 255, 0.7)", fontSize: 11, marginBottom: 4 }}>{key}</div>
-                  <div style={{ color: "#e6edf3", fontSize: 13, wordBreak: "break-word" }}>{typeof value === "object" ? JSON.stringify(value) : String(value)}</div>
-                </div>
-              ))}
-            </div>
-          ) : (
-            <div style={emptyTextStyle}>No explicit attribution metadata was found on this node.</div>
-          )}
-        </div>
-      </details>
-
-      <details style={collapseStyle}>
-        <summary style={summaryStyle}>Properties</summary>
-        <div style={{ padding: "0 14px 14px" }}>
-          {propertyEntries.length ? (
-            <div style={{ display: "flex", flexDirection: "column", gap: 8 }}>
-              {propertyEntries.map(([key, value]) => (
-                <div key={key} style={propertyCardStyle}>
-                  <div style={{ color: "rgba(88, 166, 255, 0.7)", fontSize: 11, marginBottom: 4 }}>{key}</div>
-                  <div style={{ color: "#e6edf3", fontSize: 13, wordBreak: "break-word" }}>{typeof value === "object" ? JSON.stringify(value) : String(value)}</div>
-                </div>
-              ))}
-            </div>
-          ) : (
-            <div style={emptyTextStyle}>No additional properties are attached to this node.</div>
-          )}
-        </div>
-      </details>
-    </aside>
-  );
-}
-
-export function GraphWorkspaceShell() {
-  const [selectedNodeId, setSelectedNodeId] = useState("");
-  const [selectedNodeState, setSelectedNodeState] = useState<GraphSelectedNodeState | null>(null);
-  const [isLayoutRunning, setIsLayoutRunning] = useState(false);
-  const [viewMode, setViewMode] = useState<GraphViewMode>("full");
-  const [searchQuery, setSearchQuery] = useState("");
-  const [searchResults, setSearchResults] = useState<SearchResult[]>([]);
-  const [searchError, setSearchError] = useState("");
-  const [predictionType, setPredictionType] = useState("");
-  const [predictions, setPredictions] = useState<LinkPrediction[]>([]);
-  const [pathTargetId, setPathTargetId] = useState("");
-  const [pathResult, setPathResult] = useState<PathResponse | null>(null);
-  const [activeNodeCount, setActiveNodeCount] = useState<number | null>(null);
-  const [temporalBounds, setTemporalBounds] = useState<TemporalBounds | null>(null);
-  const [scrubberTime, setScrubberTime] = useState<Date | null>(null);
-  // Deduplicates setScrubberTime calls by millisecond value — same fix as
-  // GraphWorkspace.tsx (issue #830).
-  const lastScrubberMsRef = useRef<number | null>(null);
-  const onTimeChange = useCallback((time: Date) => {
-    const ms = time.getTime();
-    if (ms === lastScrubberMsRef.current) {
-      return;
-    }
-    lastScrubberMsRef.current = ms;
-    setScrubberTime(time);
-  }, []);
-  const [loadingProgress, setLoadingProgress] = useState<GraphLoadProgress | null>(null);
-  const [isGraphStageReady, setIsGraphStageReady] = useState(false);
-  const [layoutStatus, setLayoutStatus] = useState<GraphLayoutStatus>({
-    state: "idle",
-    source: "runtime",
-    hasCoordinates: false,
-    layoutReady: false,
-    displacement: null,
-    elapsedMs: 0,
-    stableSamples: 0,
-  });
-
-  const debouncedTime = useDebounce(scrubberTime, 150);
-  const stageRef = useRef<GraphStageHandle>(null);
-  const reload = useReloadGraphData();
-  const { data: snapshot, isLoading, isFetching, isError, error } = useGraphData({ enabled: true, onProgress: setLoadingProgress });
-
-  const handleSelectedNodeStateChange = useCallback((state: GraphSelectedNodeState | null) => {
-    setSelectedNodeState(state);
-  }, []);
-
-  const handleLayoutRunningChange = useCallback((running: boolean) => {
-    setIsLayoutRunning(running);
-  }, []);
-
-  const handleActiveNodeCountChange = useCallback((count: number | null) => {
-    setActiveNodeCount(count);
-  }, []);
-
-  const handleProgressChange = useCallback((progress: GraphLoadProgress | null) => {
-    setLoadingProgress(progress);
-  }, []);
-
-  const handleRuntimeReady = useCallback(() => {
-    setIsGraphStageReady(true);
-  }, []);
-
-  const handleLayoutStatusChange = useCallback((status: GraphLayoutStatus) => {
-    setLayoutStatus(status);
-    if (status.layoutReady) {
-      setLoadingProgress(null);
-    }
-  }, []);
-
-  const [prevFetchedAt, setPrevFetchedAt] = useState(snapshot?.fetchedAt);
-  if (snapshot?.fetchedAt !== prevFetchedAt) {
-    setPrevFetchedAt(snapshot?.fetchedAt);
-    if (snapshot) {
-      setIsGraphStageReady(false);
-      setActiveNodeCount(null);
-      setLayoutStatus({
-        state: snapshot.summary.layoutReady ? "interactive" : "idle",
-        source: snapshot.summary.layoutSource ?? "runtime",
-        hasCoordinates: snapshot.summary.hasCoordinates ?? false,
-        layoutReady: snapshot.summary.layoutReady ?? false,
-        displacement: null,
-        elapsedMs: 0,
-        stableSamples: 0,
-      });
-    }
-  }
-
-  useEffect(() => {
-    let cancelled = false;
-    const loadBounds = async () => {
-      try {
-        const response = await fetch("/api/temporal/bounds");
-        if (!response.ok || cancelled) return;
-        const data: TemporalBounds = await response.json();
-        if (!cancelled) setTemporalBounds(data);
-      } catch {
-        if (!cancelled) setTemporalBounds(null);
-      }
-    };
-    void loadBounds();
-    return () => {
-      cancelled = true;
-    };
-  }, [snapshot?.summary.nodeCount, snapshot?.summary.edgeCount]);
-
-  const neighborCountMap = useMemo(() => {
-    const map = new Map<string, number>();
-    if (!snapshot) return map;
-    for (const node of snapshot.nodes) map.set(node.id, 0);
-    for (const edge of snapshot.edges) {
-      map.set(edge.source, (map.get(edge.source) ?? 0) + 1);
-      map.set(edge.target, (map.get(edge.target) ?? 0) + 1);
-    }
-    return map;
-  }, [snapshot]);
-
-  const visibleSelectedNode = useMemo(() => {
-    if (!selectedNodeId) return null;
-    if (selectedNodeState?.id === selectedNodeId) return selectedNodeState;
-    const snapshotNode = snapshot?.nodes.find((candidate) => candidate.id === selectedNodeId);
-    if (snapshotNode) return toSelectedNodeState(snapshotNode, neighborCountMap.get(snapshotNode.id) ?? 0);
-    const searchNode = searchResults.find((candidate) => candidate.node.id === selectedNodeId)?.node;
-    return searchNode
-      ? {
-          id: searchNode.id,
-          label: searchNode.content || searchNode.id,
-          content: searchNode.content || searchNode.id,
-          nodeType: searchNode.type,
-          color: "#58a6ff",
-          valid_from: null,
-          valid_until: null,
-          properties: searchNode.properties ?? {},
-          neighborCount: 0,
-          visibleNeighborCount: 0,
-          collapsedNeighborCount: 0,
-          isNeighborhoodCollapsed: false,
-          canCollapseNeighborhood: false,
-        }
-      : null;
-  }, [neighborCountMap, searchResults, selectedNodeId, selectedNodeState, snapshot]);
-
-  const focusNode = useCallback((nodeId: string) => {
-    setSelectedNodeId(nodeId);
-    setPathResult(null);
-
-    if (!nodeId) {
-      setSelectedNodeState(null);
-      setPredictions([]);
-      return;
-    }
-
-    setSearchResults([]);
-    setIsLayoutRunning(false);
-  }, []);
-
-  const handleSearch = useCallback(async () => {
-    if (!searchQuery.trim()) {
-      setSearchResults([]);
-      return;
-    }
-
-    setSearchError("");
-    try {
-      const response = await fetch("/api/graph/search", {
-        method: "POST",
-        headers: { "Content-Type": "application/json" },
-        body: JSON.stringify({ query: searchQuery, limit: 8 }),
-      });
-      if (!response.ok) {
-        throw new Error(`Search failed with status ${response.status}`);
-      }
-
-      const data = await response.json();
-      setSearchResults(data.results || []);
-      if (data.results?.length) {
-        focusNode(data.results[0].node.id);
-      }
-    } catch (searchFetchError) {
-      setSearchError(searchFetchError instanceof Error ? searchFetchError.message : "Search failed");
-    }
-  }, [focusNode, searchQuery]);
-
-  const handleRunPredictions = useCallback(async () => {
-    if (!selectedNodeId) return;
-
-    try {
-      const response = await fetch("/api/enrich/links", {
-        method: "POST",
-        headers: { "Content-Type": "application/json" },
-        body: JSON.stringify({
-          node_id: selectedNodeId,
-          top_n: 6,
-          candidate_type: predictionType || undefined,
-          min_score: 0,
-        }),
-      });
-      if (!response.ok) {
-        throw new Error(`Link prediction failed with status ${response.status}`);
-      }
-
-      const data = await response.json();
-      setPredictions(data.predictions || []);
-    } catch (predictionError) {
-      console.error("[GraphWorkspaceShell] prediction failed", predictionError);
-      setPredictions([]);
-    }
-  }, [predictionType, selectedNodeId]);
-
-  const handleTracePath = useCallback(async () => {
-    if (!selectedNodeId || !pathTargetId.trim()) return;
-
-    try {
-      const pathParams = new URLSearchParams({
-        source: selectedNodeId,
-        target: pathTargetId.trim(),
-        algorithm: "dijkstra",
-      });
-      const response = await fetch(
-        `/api/graph/path?${pathParams.toString()}`,
-      );
-      if (!response.ok) {
-        throw new Error(`Path lookup failed with status ${response.status}`);
-      }
-
-      const data: PathResponse = await response.json();
-      setPathResult(data);
-      if (data.path?.length) {
-        const lastStep = data.path[data.path.length - 1];
-        stageRef.current?.focusNode(lastStep);
-      }
-    } catch (pathError) {
-      console.error("[GraphWorkspaceShell] path trace failed", pathError);
-      setPathResult(null);
-    }
-  }, [pathTargetId, selectedNodeId]);
-
-  const handleDownloadProvenance = useCallback(async (format: "json" | "markdown") => {
-    if (!selectedNodeId) return;
-
-    const suffix = format === "markdown" ? "markdown" : "json";
-    const response = await fetch(`/api/provenance/report?node_id=${encodeURIComponent(selectedNodeId)}&format=${suffix}`);
-    if (!response.ok) {
-      throw new Error(`Provenance report failed with status ${response.status}`);
-    }
-
-    const blob = await response.blob();
-    const url = window.URL.createObjectURL(blob);
-    const anchor = document.createElement("a");
-    anchor.href = url;
-    anchor.download = `${selectedNodeId}_provenance.${format === "markdown" ? "md" : "json"}`;
-    document.body.appendChild(anchor);
-    anchor.click();
-    window.URL.revokeObjectURL(url);
-    document.body.removeChild(anchor);
-  }, [selectedNodeId]);
-
-  const searchSummary = useMemo(() => {
-    if (!searchResults.length) return null;
-    return `${searchResults.length} search result${searchResults.length === 1 ? "" : "s"}`;
-  }, [searchResults.length]);
-
-  const focusedSummary = useMemo(() => {
-    if (!visibleSelectedNode) return null;
-    if (viewMode === "focused") {
-      const visibleNeighbors = Math.min(visibleSelectedNode.neighborCount, 16);
-      return `${visibleNeighbors + 1} nodes in focused view`;
-    }
-    return `${visibleSelectedNode.neighborCount} direct neighbors highlighted`;
-  }, [viewMode, visibleSelectedNode]);
-
-  const requestViewMode = useCallback((nextViewMode: GraphViewMode) => {
-    if (nextViewMode === "focused") {
-      if (!selectedNodeId) {
-        return;
-      }
-      setViewMode("focused");
-      setIsLayoutRunning(false);
-      return;
-    }
-
-    setViewMode("full");
-  }, [selectedNodeId]);
-
-  const showLoadingOverlay =
-    isLoading
-    || isFetching
-    || !isGraphStageReady
-    || (layoutStatus.source === "runtime" && !layoutStatus.layoutReady && !selectedNodeId && viewMode === "full");
-
-  const layoutStatusLabel = useMemo(() => {
-    if (layoutStatus.source === "provided" && layoutStatus.layoutReady) return "Persisted layout";
-    if (layoutStatus.source === "carried" && layoutStatus.layoutReady) return "Preserved layout";
-    if (layoutStatus.state === "bootstrapping") return "Bootstrapping layout";
-    if (layoutStatus.state === "running") return "Stabilizing layout";
-    if (layoutStatus.state === "failed") return "Layout timeout fallback";
-    return null;
-  }, [layoutStatus]);
-
-  return (
-    <div className="palantir-bg" style={{ position: "relative", width: "100%", height: "100%", overflow: "hidden", display: "flex", flexDirection: "column" }}>
-      <style>{HUD_CSS}</style>
-      <div className="palantir-grid" />
-      <div className="palantir-vignette" />
-
-      <div style={{ flex: 1, position: "relative", zIndex: 3, minHeight: 0 }}>
-        <Suspense fallback={null}>
-          <GraphRuntimeStage
-            ref={stageRef}
-            snapshot={snapshot}
-            selectedNodeId={selectedNodeId}
-            activePath={pathResult?.path ?? []}
-            onNodeSelect={focusNode}
-            onSelectedNodeStateChange={handleSelectedNodeStateChange}
-            isLayoutRunning={isLayoutRunning}
-            onLayoutRunningChange={handleLayoutRunningChange}
-            viewMode={viewMode}
-            temporalTime={debouncedTime}
-            onActiveNodeCountChange={handleActiveNodeCountChange}
-            onProgressChange={handleProgressChange}
-            onLayoutStatusChange={handleLayoutStatusChange}
-            onRuntimeReady={handleRuntimeReady}
-          />
-        </Suspense>
-        <GraphLoadingOverlay
-          progress={loadingProgress}
-          visible={showLoadingOverlay}
-          showGraphBehind={Boolean(loadingProgress?.showGraphBehind || isGraphStageReady)}
-        />
-      </div>
-
-      <Suspense fallback={<TimelineFallback min={temporalBounds?.min ?? null} max={temporalBounds?.max ?? null} />}>
-        <TimelinePanel
-          onTimeChange={onTimeChange}
-          minDate={temporalBounds?.min ?? undefined}
-          maxDate={temporalBounds?.max ?? undefined}
-        />
-      </Suspense>
-
-      <div style={{ position: "absolute", inset: 0, pointerEvents: "none", zIndex: 10 }}>
-        <div className="graph-shell-top">
-          <section className="graph-status-card">
-            <div className="graph-status-label">Graph Studio</div>
-            <div className="graph-status-title">{visibleSelectedNode ? visibleSelectedNode.label : "Knowledge Explorer"}</div>
-            <div className="graph-status-metrics">
-              {showLoadingOverlay && loadingProgress ? <span style={{ ...metricPillStyle, color: "#a9ddff" }}>{getGraphLoadTitle(loadingProgress.phase)}</span> : null}
-              {layoutStatusLabel ? <span style={{ ...metricPillStyle, color: "#a9ddff" }}>{layoutStatusLabel}</span> : null}
-              {snapshot ? <span style={metricPillStyle}>{snapshot.summary.nodeCount.toLocaleString()} nodes · {snapshot.summary.edgeCount.toLocaleString()} edges</span> : null}
-              {activeNodeCount !== null ? <span style={{ ...metricPillStyle, color: "#4fd49c", borderColor: "rgba(79, 212, 156, 0.22)" }}>{activeNodeCount.toLocaleString()} active</span> : null}
-              {searchSummary ? <span style={metricPillStyle}>{searchSummary}</span> : null}
-              {focusedSummary ? <span style={{ ...metricPillStyle, color: "#f2b66d", borderColor: "rgba(242, 182, 109, 0.24)" }}>{focusedSummary}</span> : null}
-              {isError ? <span style={{ ...metricPillStyle, color: "#ff8f85", borderColor: "rgba(255, 123, 114, 0.22)" }}>{(error as Error).message}</span> : null}
-            </div>
-          </section>
-
-          <section className="graph-command-card">
-            <div className="graph-command-row">
-              <div className="graph-toggle-cluster">
-              {selectedNodeId ? (
-                  <>
-                    <button onClick={() => requestViewMode("focused")} style={{ ...actionButtonStyle, background: viewMode === "focused" ? "rgba(31, 111, 235, 0.38)" : actionButtonStyle.background, borderColor: viewMode === "focused" ? "rgba(127, 208, 255, 0.42)" : "rgba(88, 166, 255, 0.2)" }}>Focused View</button>
-                    <button onClick={() => requestViewMode("full")} style={{ ...actionButtonStyle, background: viewMode === "full" ? "rgba(31, 111, 235, 0.38)" : actionButtonStyle.background, borderColor: viewMode === "full" ? "rgba(127, 208, 255, 0.42)" : "rgba(88, 166, 255, 0.2)" }}>Full Graph</button>
-                  </>
-                ) : (
-                  <span style={{ color: "#7f95b3", fontSize: 12 }}>Select a node to switch graph views</span>
-                )}
-              </div>
-
-              <div className="graph-action-cluster">
-                <button onClick={() => setIsLayoutRunning((value) => !value)} style={secondaryActionButtonStyle} disabled={isLoading || isFetching}>
-                  {isLayoutRunning ? "Pause Layout" : "Run Layout"}
-                </button>
-                <button onClick={() => { setIsGraphStageReady(false); reload(); }} style={secondaryActionButtonStyle} disabled={isLoading || isFetching}>
-                  Reload
-                </button>
-              </div>
-            </div>
-
-            <div className="graph-command-row">
-              <div className="graph-search-shell">
-                <input
-                  value={searchQuery}
-                  onChange={(event) => setSearchQuery(event.target.value)}
-                  onKeyDown={(event) => {
-                    if (event.key === "Enter") {
-                      void handleSearch();
-                    }
-                  }}
-                  placeholder="Search a node, e.g. Metformin"
-                  style={{ ...inputStyle, minWidth: 260 }}
-                  disabled={showLoadingOverlay && !selectedNodeId}
-                />
-                <button onClick={() => void handleSearch()} style={actionButtonStyle} disabled={showLoadingOverlay && !selectedNodeId}>Search</button>
-              </div>
-            </div>
-          </section>
-        </div>
-
-        {searchError ? <div style={{ position: "absolute", top: 144, right: 34, color: "#ff7b72", fontSize: 12, pointerEvents: "auto" }}>{searchError}</div> : null}
-        {searchResults.length ? (
-          <div className="graph-search-results hud-scrollbar">
-            <div className="graph-search-results-label">Search Results</div>
-            <div style={{ display: "flex", flexDirection: "column", gap: 8 }}>
-              {searchResults.map((result) => (
-                <button key={result.node.id} className="graph-search-result-card" onClick={() => focusNode(result.node.id)}>
-                  <div style={{ color: "#fff", fontWeight: 700 }}>{result.node.content || result.node.id}</div>
-                  <div style={{ color: "#8b949e", fontSize: 12 }}>{result.node.type}</div>
-                  <div style={{ color: "#58a6ff", fontSize: 12, marginTop: 4 }}>score {result.score.toFixed(3)}</div>
-                </button>
-              ))}
-            </div>
-          </div>
-        ) : null}
-
-        <div className="graph-inspector hud-scrollbar" data-open={selectedNodeId ? "true" : "false"}>
-          <NodePanel
-            node={visibleSelectedNode}
-            predictions={predictions}
-            predictionType={predictionType}
-            onPredictionTypeChange={setPredictionType}
-            onRunPredictions={() => void handleRunPredictions()}
-            pathTargetId={pathTargetId}
-            onPathTargetChange={setPathTargetId}
-            onTracePath={() => void handleTracePath()}
-            pathResult={pathResult}
-            onDownloadProvenance={(format) => void handleDownloadProvenance(format)}
-          />
-        </div>
-      </div>
-    </div>
-  );
-}
-
-const metricPillStyle: CSSProperties = {
-  background: "rgba(88, 166, 255, 0.08)",
-  color: "#8ed3ff",
-  padding: "6px 11px",
-  borderRadius: 999,
-  fontSize: 12,
-  fontWeight: 700,
-  border: "1px solid rgba(88, 166, 255, 0.14)",
-};
-
-const sectionStyle: CSSProperties = {
-  display: "flex",
-  flexDirection: "column",
-  gap: 10,
-  padding: 14,
-  background: "linear-gradient(180deg, rgba(255,255,255,0.025), rgba(255,255,255,0.01))",
-  border: "1px solid rgba(255, 255, 255, 0.06)",
-  borderRadius: 16,
-};
-
-const sectionTitleStyle: CSSProperties = {
-  color: "#8fa8c6",
-  fontSize: 11,
-  fontWeight: 800,
-  textTransform: "uppercase",
-  letterSpacing: "0.08em",
-};
-
-const inputStyle: CSSProperties = {
-  width: "100%",
-  background: "rgba(0, 0, 0, 0.24)",
-  border: "1px solid rgba(88, 166, 255, 0.14)",
-  color: "#fff",
-  borderRadius: 12,
-  padding: "10px 12px",
-  fontSize: 13,
-};
-
-const actionButtonStyle: CSSProperties = {
-  background: "linear-gradient(180deg, rgba(53, 130, 245, 0.28), rgba(25, 88, 185, 0.18))",
-  color: "#fff",
-  border: "1px solid rgba(88, 166, 255, 0.2)",
-  borderRadius: 12,
-  padding: "10px 13px",
-  cursor: "pointer",
-  fontWeight: 700,
-  fontSize: 12,
-  display: "inline-flex",
-  alignItems: "center",
-  justifyContent: "center",
-  boxShadow: "inset 0 1px 0 rgba(255,255,255,0.05)",
-};
-
-const secondaryActionButtonStyle: CSSProperties = {
-  ...actionButtonStyle,
-  background: "rgba(255, 255, 255, 0.035)",
-  border: "1px solid rgba(255, 255, 255, 0.06)",
-  color: "#d6e5f8",
-  fontWeight: 500,
-};
-
-const predictionCardStyle: CSSProperties = {
-  textAlign: "left",
-  padding: 12,
-  background: "rgba(88, 166, 255, 0.06)",
-  border: "1px solid rgba(88, 166, 255, 0.1)",
-  borderRadius: 14,
-  cursor: "pointer",
-};
-
-const pathStepStyle: CSSProperties = {
-  color: "#e6edf3",
-  fontSize: 13,
-  padding: "8px 10px",
-  background: "rgba(255, 255, 255, 0.03)",
-  borderRadius: 8,
-};
-
-const propertyCardStyle: CSSProperties = {
-  background: "rgba(0, 0, 0, 0.18)",
-  padding: "10px 12px",
-  borderRadius: 12,
-  border: "1px solid rgba(255, 255, 255, 0.05)",
-};
-
-const emptyTextStyle: CSSProperties = {
-  color: "#8b949e",
-  fontSize: 12,
-  lineHeight: 1.5,
-};
-
-const subtleChipStyle: CSSProperties = {
-  background: "rgba(255, 255, 255, 0.035)",
-  color: "#9fb6d2",
-  padding: "5px 9px",
-  borderRadius: 999,
-  fontSize: 11,
-  border: "1px solid rgba(255, 255, 255, 0.06)",
-};
-
-const collapseStyle: CSSProperties = {
-  border: "1px solid rgba(255, 255, 255, 0.05)",
-  borderRadius: 14,
-  background: "rgba(0, 0, 0, 0.14)",
-  overflow: "hidden",
-};
-
-const summaryStyle: CSSProperties = {
-  cursor: "pointer",
-  listStyle: "none",
-  padding: "12px 14px",
-  color: "#c6d4e3",
-  fontSize: 12,
-  fontWeight: 700,
-  letterSpacing: "0.04em",
-  textTransform: "uppercase",
-};

explorer/src/workspaces/GraphWorkspace/MarkdownContentViewer.tsx

@@ -0,0 +1,404 @@
+import { useState, useRef, useEffect, useMemo, type CSSProperties } from "react";
+import ReactMarkdown, { type Components } from "react-markdown";
+import remarkGfm from "remark-gfm";
+import { Check, Copy, Code2, Eye, ExternalLink, Image as ImageIcon } from "lucide-react";
+import { GRAPH_THEME } from "./graphTheme";
+import { isSafeUrl } from "./markdownUrlSafety";
+
+export interface MarkdownContentViewerProps {
+  content?: string | null;
+  className?: string;
+  defaultMode?: "preview" | "source";
+}
+
+export function MarkdownContentViewer({
+  content,
+  className,
+  defaultMode = "preview",
+}: MarkdownContentViewerProps) {
+  const [activeMode, setActiveMode] = useState<"preview" | "source">(defaultMode);
+  const [copied, setCopied] = useState(false);
+  // Track the content value for which the copied indicator is valid.
+  // When content changes (i.e. the user selects a different node), reset the
+  // copied indicator inline during render rather than in a useEffect — this
+  // avoids a cascading-render lint error and is the React-recommended pattern
+  // for resetting derived visual state on prop changes.
+  const [copiedForContent, setCopiedForContent] = useState<string | null | undefined>(content);
+  if (copiedForContent !== content) {
+    setCopiedForContent(content);
+    if (copied) {
+      // Clear the stale indicator synchronously so the new node's copy button
+      // never shows "Copied" from the previous selection.
+      setCopied(false);
+    }
+  }
+
+  const copyTimeoutRef = useRef<ReturnType<typeof setTimeout> | null>(null);
+
+  // Clean up any outstanding timeout on unmount.
+  useEffect(() => {
+    return () => {
+      if (copyTimeoutRef.current) {
+        clearTimeout(copyTimeoutRef.current);
+      }
+    };
+  }, []);
+
+  const rawContent = typeof content === "string" ? content : "";
+  const hasContent = rawContent.trim().length > 0;
+
+  // react-markdown runs the whole remark pipeline synchronously inside its own
+  // render, so without this memo every unrelated re-render of this component --
+  // clicking Copy, toggling Preview/Source -- re-parses the entire document.
+  // Measured at ~364ms per re-render for a 1000-row GFM table (issue #1118).
+  // Keyed on rawContent so a genuine node change still re-parses exactly once.
+  const renderedMarkdown = useMemo(
+    () => (
+      <ReactMarkdown remarkPlugins={REMARK_PLUGINS} components={MARKDOWN_COMPONENTS}>
+        {rawContent}
+      </ReactMarkdown>
+    ),
+    [rawContent],
+  );
+
+  const handleCopy = async () => {
+    if (!hasContent) return;
+    try {
+      await navigator.clipboard.writeText(rawContent);
+      if (copyTimeoutRef.current) {
+        clearTimeout(copyTimeoutRef.current);
+      }
+      setCopied(true);
+      copyTimeoutRef.current = setTimeout(() => setCopied(false), 1500);
+    } catch {
+      // Clipboard write unavailable
+    }
+  };
+
+  return (
+    <div className={className} style={viewerContainerStyle}>
+      <div style={viewerHeaderStyle}>
+        <div style={{ display: "flex", gap: 4 }} role="tablist">
+          <button
+            type="button"
+            role="tab"
+            aria-selected={activeMode === "preview"}
+            onClick={() => setActiveMode("preview")}
+            style={{ ...tabBtnStyle, ...(activeMode === "preview" ? activeTabBtnStyle : {}) }}
+          >
+            <Eye size={12} style={{ marginRight: 5 }} />
+            Preview
+          </button>
+          <button
+            type="button"
+            role="tab"
+            aria-selected={activeMode === "source"}
+            onClick={() => setActiveMode("source")}
+            style={{ ...tabBtnStyle, ...(activeMode === "source" ? activeTabBtnStyle : {}) }}
+          >
+            <Code2 size={12} style={{ marginRight: 5 }} />
+            Source
+          </button>
+        </div>
+
+        {hasContent && (
+          <button type="button" onClick={() => void handleCopy()} style={copyBtnStyle} title="Copy raw content">
+            {copied ? (
+              <>
+                <Check size={12} color="#3fb950" style={{ marginRight: 4 }} />
+                <span style={{ color: "#3fb950", fontSize: 11 }}>Copied</span>
+              </>
+            ) : (
+              <>
+                <Copy size={12} style={{ marginRight: 4 }} />
+                <span style={{ fontSize: 11 }}>Copy</span>
+              </>
+            )}
+          </button>
+        )}
+      </div>
+
+      <div style={viewerBodyStyle}>
+        {!hasContent ? (
+          <div style={emptyTextStyle}>No content available for this node.</div>
+        ) : activeMode === "source" ? (
+          <pre style={sourcePreStyle}>
+            <code style={sourceCodeStyle}>{rawContent}</code>
+          </pre>
+        ) : (
+          <div style={previewStyle}>{renderedMarkdown}</div>
+        )}
+      </div>
+    </div>
+  );
+}
+
+/* ─── Markdown rendering config ───────────────────────────────────── */
+
+// Both props are hoisted to module scope so they keep a stable identity across
+// renders. As inline literals they allocated a fresh plugin array and ~20 fresh
+// arrow components on every render, which made React treat every mapped tag as a
+// new element type and remount the entire rendered subtree instead of updating
+// it (issue #1118). The arrow bodies only read the style constants below at call
+// time, so declaring the map before them is safe.
+const REMARK_PLUGINS = [remarkGfm];
+
+const MARKDOWN_COMPONENTS: Components = {
+  // C-1: react-markdown passes a HAST `node` prop (the raw AST
+  // Element) to every custom component override via passNode:true.
+  // In React 19 any unknown prop spreads onto a native element are
+  // serialised as HTML attributes, producing node="[object Object]"
+  // on every rendered link. Fix: destructure `node` by name so it
+  // is explicitly discarded, then spread `...rest` to preserve all
+  // other legitimate HAST/remark-gfm attributes — e.g. the `id`,
+  // `aria-describedby`, `aria-label`, `data-footnote-ref`,
+  // `data-footnote-backref`, and `class` attrs that GFM footnotes
+  // require for correct in-page navigation and accessibility.
+  //
+  // C-2: fragment links (#anchor, GFM footnote backlinks) must
+  // navigate within the current document. External links continue
+  // to use target="_blank" with noopener noreferrer.
+  //
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  a: ({ href, children, title, node: _node, ...rest }) => {
+    if (!isSafeUrl(href)) {
+      return <span style={{ color: GRAPH_THEME.ui.text.muted, textDecoration: "line-through" }}>{children}</span>;
+    }
+    // isSafeUrl returning true guarantees href is a non-empty string.
+    const safeHref = href ?? "";
+    // Fragment links (#section, footnote backlinks like
+    // #user-content-fnref-1) are in-document anchors. Opening them
+    // in a new tab would break GFM footnote back-navigation.
+    const isFragment = safeHref.startsWith("#");
+    if (isFragment) {
+      return (
+        <a href={safeHref} title={title} style={linkStyle} {...rest}>
+          {children}
+        </a>
+      );
+    }
+    return (
+      <a href={safeHref} title={title} target="_blank" rel="noopener noreferrer" style={linkStyle} {...rest}>
+        {children}
+        <ExternalLink size={10} style={{ marginLeft: 3, verticalAlign: "middle", display: "inline" }} />
+      </a>
+    );
+  },
+  img: ({ src, alt }) => (
+    <span style={imageBadgeStyle} title={src || "Image"}>
+      <ImageIcon size={12} style={{ marginRight: 5 }} />
+      <span>Image: {alt || src || "unlabeled"}</span>
+    </span>
+  ),
+  h1: ({ children }) => <h1 style={h1Style}>{children}</h1>,
+  h2: ({ children }) => <h2 style={h2Style}>{children}</h2>,
+  h3: ({ children }) => <h3 style={h3Style}>{children}</h3>,
+  h4: ({ children }) => <h4 style={h4Style}>{children}</h4>,
+  p: ({ children }) => <p style={{ margin: "0 0 8px 0" }}>{children}</p>,
+  ul: ({ children }) => <ul style={{ margin: "0 0 8px 0", paddingLeft: 18 }}>{children}</ul>,
+  ol: ({ children }) => <ol style={{ margin: "0 0 8px 0", paddingLeft: 18 }}>{children}</ol>,
+  li: ({ children }) => <li style={{ marginBottom: 3 }}>{children}</li>,
+  blockquote: ({ children }) => <blockquote style={blockquoteStyle}>{children}</blockquote>,
+  hr: () => <hr style={{ border: "none", borderTop: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`, margin: "10px 0" }} />,
+  table: ({ children }) => (
+    <div style={{ width: "100%", overflowX: "auto", margin: "8px 0", borderRadius: 6, border: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}` }}>
+      <table style={{ width: "100%", borderCollapse: "collapse", fontSize: 12 }}>{children}</table>
+    </div>
+  ),
+  thead: ({ children }) => <thead style={{ background: "rgba(255, 255, 255, 0.04)" }}>{children}</thead>,
+  tbody: ({ children }) => <tbody>{children}</tbody>,
+  tr: ({ children }) => <tr style={{ borderBottom: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}` }}>{children}</tr>,
+  th: ({ children }) => <th style={{ padding: "6px 8px", textAlign: "left", fontWeight: 700, color: GRAPH_THEME.ui.text.strong, borderRight: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}` }}>{children}</th>,
+  td: ({ children }) => <td style={{ padding: "6px 8px", color: GRAPH_THEME.ui.text.body, borderRight: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}` }}>{children}</td>,
+  pre: ({ children }) => <pre style={preBlockStyle}>{children}</pre>,
+  // C-1: discard `node` here too — code elements are custom components
+  // and would otherwise receive node="[object Object]" in the DOM.
+  code: ({ className: codeClass, children }) => {
+    const isInline = !codeClass && typeof children === "string" && !children.includes("\n");
+    return (
+      <code style={isInline ? inlineCodeStyle : blockCodeStyle}>
+        {children}
+      </code>
+    );
+  },
+};
+
+/* ─── Styles ──────────────────────────────────────────────────────── */
+
+const viewerContainerStyle: CSSProperties = {
+  display: "flex",
+  flexDirection: "column",
+  background: "rgba(255, 255, 255, 0.025)",
+  border: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
+  borderRadius: 12,
+  overflow: "hidden",
+};
+
+const viewerHeaderStyle: CSSProperties = {
+  display: "flex",
+  alignItems: "center",
+  justifyContent: "space-between",
+  padding: "6px 10px",
+  background: "rgba(0, 0, 0, 0.2)",
+  borderBottom: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
+};
+
+const tabBtnStyle: CSSProperties = {
+  display: "inline-flex",
+  alignItems: "center",
+  padding: "4px 9px",
+  borderRadius: 6,
+  border: "1px solid transparent",
+  background: "transparent",
+  color: GRAPH_THEME.ui.text.muted,
+  fontSize: 12,
+  fontWeight: 600,
+  cursor: "pointer",
+  transition: "all 150ms ease",
+};
+
+const activeTabBtnStyle: CSSProperties = {
+  background: GRAPH_THEME.ui.timeline.playheadSoft,
+  border: `1px solid ${GRAPH_THEME.ui.control.activeBorder}`,
+  color: GRAPH_THEME.ui.timeline.playhead,
+};
+
+const copyBtnStyle: CSSProperties = {
+  display: "inline-flex",
+  alignItems: "center",
+  padding: "3px 8px",
+  borderRadius: 6,
+  border: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
+  background: "rgba(255, 255, 255, 0.04)",
+  color: GRAPH_THEME.ui.text.subtle,
+  fontSize: 11,
+  cursor: "pointer",
+};
+
+const viewerBodyStyle: CSSProperties = {
+  padding: 12,
+  maxHeight: 380,
+  overflowY: "auto",
+};
+
+const emptyTextStyle: CSSProperties = {
+  color: GRAPH_THEME.ui.text.muted,
+  fontSize: 12,
+  lineHeight: 1.5,
+  fontStyle: "italic",
+};
+
+const sourcePreStyle: CSSProperties = {
+  margin: 0,
+  padding: 10,
+  borderRadius: 8,
+  background: "rgba(0, 0, 0, 0.3)",
+  border: "1px solid rgba(255, 255, 255, 0.05)",
+  overflowX: "auto",
+};
+
+const sourceCodeStyle: CSSProperties = {
+  fontFamily: "'JetBrains Mono', 'Fira Code', monospace",
+  fontSize: 12,
+  lineHeight: 1.6,
+  color: GRAPH_THEME.ui.text.strong,
+  whiteSpace: "pre-wrap",
+  wordBreak: "break-word",
+  userSelect: "text",
+};
+
+const previewStyle: CSSProperties = {
+  color: GRAPH_THEME.ui.text.body,
+  fontSize: 13,
+  lineHeight: 1.6,
+  wordBreak: "break-word",
+};
+
+const h1Style: CSSProperties = {
+  fontSize: 16,
+  fontWeight: 700,
+  color: GRAPH_THEME.ui.text.strong,
+  marginTop: 8,
+  marginBottom: 6,
+  paddingBottom: 3,
+  borderBottom: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
+};
+
+const h2Style: CSSProperties = {
+  fontSize: 14,
+  fontWeight: 700,
+  color: GRAPH_THEME.ui.text.strong,
+  marginTop: 8,
+  marginBottom: 4,
+};
+
+const h3Style: CSSProperties = {
+  fontSize: 13,
+  fontWeight: 600,
+  color: GRAPH_THEME.ui.text.strong,
+  marginTop: 6,
+  marginBottom: 4,
+};
+
+const h4Style: CSSProperties = {
+  fontSize: 12,
+  fontWeight: 600,
+  color: GRAPH_THEME.ui.text.strong,
+  marginTop: 4,
+  marginBottom: 2,
+};
+
+const blockquoteStyle: CSSProperties = {
+  margin: "8px 0",
+  padding: "6px 12px",
+  borderLeft: `3px solid ${GRAPH_THEME.ui.timeline.playhead}`,
+  background: "rgba(98, 226, 205, 0.05)",
+  borderRadius: "0 6px 6px 0",
+  color: GRAPH_THEME.ui.text.body,
+  fontStyle: "italic",
+};
+
+const linkStyle: CSSProperties = {
+  color: "#79c0ff",
+  textDecoration: "underline",
+  textUnderlineOffset: "3px",
+  wordBreak: "break-all",
+};
+
+const imageBadgeStyle: CSSProperties = {
+  display: "inline-flex",
+  alignItems: "center",
+  padding: "3px 7px",
+  background: "rgba(255, 255, 255, 0.04)",
+  border: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
+  borderRadius: 6,
+  color: GRAPH_THEME.ui.text.muted,
+  fontSize: 11,
+  margin: "3px 0",
+};
+
+const inlineCodeStyle: CSSProperties = {
+  fontFamily: "'JetBrains Mono', monospace",
+  fontSize: 12,
+  padding: "2px 5px",
+  borderRadius: 4,
+  background: "rgba(255, 255, 255, 0.07)",
+  color: "#e6edf3",
+  border: "1px solid rgba(255, 255, 255, 0.08)",
+};
+
+const preBlockStyle: CSSProperties = {
+  margin: "8px 0",
+  padding: 10,
+  borderRadius: 8,
+  background: "rgba(0, 0, 0, 0.35)",
+  border: "1px solid rgba(255, 255, 255, 0.08)",
+  overflowX: "auto",
+};
+
+const blockCodeStyle: CSSProperties = {
+  fontFamily: "'JetBrains Mono', monospace",
+  fontSize: 12,
+  lineHeight: 1.5,
+  color: "#e6edf3",
+};

explorer/src/workspaces/GraphWorkspace/graphSceneState.ts

@@ -2099,6 +2099,15 @@ function createCollapsedNeighborhoodGraph(
   return collapsedGraph;
 }
 
+// Normalize an edge relationship type: empty string, null, and undefined all
+// fall back to the project-wide default used consistently across every
+// aggregation path. Keep this local — it exists only to guarantee that the
+// three code paths (single-entry, multi-entry, community-grouped) produce the
+// same semantics and do not diverge again.
+function normalizeEdgeType(value: string | null | undefined): string {
+  return value || "related_to";
+}
+
 function aggregateDisplayGraph(graphRef: GraphRef): Graph<NodeAttributes, EdgeAttributes> {
   const aggregated = new Graph<NodeAttributes, EdgeAttributes>({
     type: "directed",
@@ -2124,10 +2133,13 @@ function aggregateDisplayGraph(graphRef: GraphRef): Graph<NodeAttributes, EdgeAt
       const [{ edgeId, attrs }] = entries;
       aggregated.mergeDirectedEdgeWithKey(edgeId, sourceId, targetId, {
         ...attrs,
+        // #1009: normalize empty/null/undefined edgeType so Sigma's label
+        // renderer never receives a blank string on the single-entry path.
+        edgeType: normalizeEdgeType(attrs.edgeType),
+        dominantEdgeType: normalizeEdgeType(attrs.dominantEdgeType ?? attrs.edgeType),
         rawEdgeIds: collectRawEdgeIds(attrs, edgeId),
         isAggregated: isAggregatedEdgeAttributes(attrs),
         aggregateCount: attrs.aggregateCount ?? collectRawEdgeIds(attrs, edgeId).length,
-        dominantEdgeType: attrs.dominantEdgeType ?? attrs.edgeType,
         representativeWeight: attrs.representativeWeight ?? Number(attrs.weight ?? 1),
       });
       return;
@@ -2150,10 +2162,11 @@ function aggregateDisplayGraph(graphRef: GraphRef): Graph<NodeAttributes, EdgeAt
     const rawEdgeIds = entries.flatMap(({ edgeId, attrs }) => collectRawEdgeIds(attrs, edgeId));
     const typeCounts = new Map<string, number>();
     entries.forEach(({ attrs }) => {
-      const edgeType = String(attrs.edgeType ?? "related_to");
+      const edgeType = normalizeEdgeType(attrs.edgeType);
       typeCounts.set(edgeType, (typeCounts.get(edgeType) ?? 0) + 1);
     });
-    const dominantEdgeType = [...typeCounts.entries()].sort((left, right) => right[1] - left[1])[0]?.[0] ?? representative.attrs.edgeType ?? "related_to";
+    const dominantEdgeType = [...typeCounts.entries()].sort((left, right) => right[1] - left[1])[0]?.[0]
+      ?? normalizeEdgeType(representative.attrs.edgeType);
     const reverseKey = `${targetId}→${sourceId}`;
     const isBidirectionalBundle = groupedEdges.has(reverseKey);
     const syntheticEdgeId = `${AGGREGATED_EDGE_PREFIX}${sourceId}::${targetId}`;
@@ -2167,10 +2180,10 @@ function aggregateDisplayGraph(graphRef: GraphRef): Graph<NodeAttributes, EdgeAt
       rawEdgeIds,
       isAggregated: true,
       aggregateCount: rawEdgeIds.length,
-      dominantEdgeType: String(dominantEdgeType),
+      dominantEdgeType: dominantEdgeType,
       representativeWeight: Number(representative.attrs.weight ?? 1),
       weight: Number(representative.attrs.weight ?? 1),
-      edgeType: String(representative.attrs.edgeType ?? dominantEdgeType ?? "related_to"),
+      edgeType: representative.attrs.edgeType || dominantEdgeType,
       parallelCount: rawEdgeIds.length,
       familySize: rawEdgeIds.length,
       bundleKind: isBidirectionalBundle ? "bidirectional" : "parallel",
@@ -2280,7 +2293,7 @@ function buildCommunityGroupedGraph(): GraphDisplayResult {
     };
     bucket.rawEdgeIds.push(String(edgeId));
     bucket.weight = Math.max(bucket.weight, Number((attrs as EdgeAttributes).weight ?? 1));
-    const edgeType = String((attrs as EdgeAttributes).edgeType ?? "related_to");
+    const edgeType = normalizeEdgeType((attrs as EdgeAttributes).edgeType);
     bucket.typeCounts.set(edgeType, (bucket.typeCounts.get(edgeType) ?? 0) + 1);
     groupedEdges.set(key, bucket);
   });
@@ -2396,7 +2409,8 @@ function buildCommunityGroupedGraph(): GraphDisplayResult {
     if (!visibleGroupedEdgeKeys.has(key)) {
       return;
     }
-    const dominantEdgeType = [...bundle.typeCounts.entries()].sort((left, right) => right[1] - left[1])[0]?.[0] ?? "related_to";
+    const dominantEdgeType = [...bundle.typeCounts.entries()].sort((left, right) => right[1] - left[1])[0]?.[0]
+      ?? "related_to";
     const reverseKey = `${bundle.targetId}→${bundle.sourceId}`;
     const syntheticEdgeId = `${AGGREGATED_EDGE_PREFIX}${key}`;
     const aggregateCount = bundle.rawEdgeIds.length;

explorer/src/workspaces/GraphWorkspace/markdownUrlSafety.ts

@@ -0,0 +1,29 @@
+/**
+ * URL-safety predicate for the Markdown content viewer.
+ *
+ * Extracted into a pure module so the check can be unit-tested without
+ * importing the MarkdownContentViewer React component, and so the component
+ * module exports only components (react-refresh/only-export-components,
+ * issue #1119). The behaviour is unchanged from the original in-component
+ * implementation: only http, https, mailto, in-document fragments, and
+ * root-relative paths are permitted.
+ */
+
+export function isSafeUrl(url?: string): boolean {
+  if (!url) return false;
+  const trimmed = url.trim();
+  // Reject whitespace-only strings — new URL("", base) would resolve to the base
+  // protocol and produce a false positive. This guards direct callers of the exported
+  // function; markdown parsers normalise whitespace-only destinations to "" which
+  // already fails the !url check above.
+  if (!trimmed) return false;
+  if (trimmed.startsWith("//")) return false;
+  if (trimmed.startsWith("#")) return true;
+  if (trimmed.startsWith("/")) return true;
+  try {
+    const parsed = new URL(trimmed, "http://localhost");
+    return ["http:", "https:", "mailto:"].includes(parsed.protocol);
+  } catch {
+    return false;
+  }
+}

explorer/src/workspaces/GraphWorkspace/plugins/explorationEffectsPlugin.tsx

@@ -1,6 +1,7 @@
 import type { CSSProperties } from "react";
 
 import type {
+  GraphDiagnosticsSnapshot,
   GraphEffectAvailability,
   GraphEffectToggle,
 } from "../types";
@@ -30,6 +31,11 @@ const EFFECT_ROWS: EffectRowConfig[] = [
     label: "Neighborhood Lens",
     description: "Local emphasis around the hovered or selected node.",
   },
+  {
+    key: "edgeLabelsEnabled",
+    label: "Edge Labels",
+    description: "Draw the relationship type on graph edges. Off restores label-free edges on dense graphs.",
+  },
   {
     key: "legendEnabled",
     label: "Semantic Legend",
@@ -37,6 +43,17 @@ const EFFECT_ROWS: EffectRowConfig[] = [
   },
 ];
 
+// Maps the effect toggle keys rendered by this plugin to their corresponding
+// availability keys in GraphDiagnosticsSnapshot["effectAvailability"]. Kept
+// local because this plugin only renders a subset of all effects.
+const EFFECT_AVAILABILITY_KEYS: Partial<Record<GraphEffectToggle, keyof GraphDiagnosticsSnapshot["effectAvailability"]>> = {
+  pathPulseEnabled: "pathPulse",
+  pathFlowEnabled: "pathFlow",
+  lensEnabled: "lens",
+  edgeLabelsEnabled: "edgeLabels",
+  legendEnabled: "legend",
+};
+
 function renderAvailabilityText(availability: GraphEffectAvailability) {
   if (availability.available) {
     if (typeof availability.visibleSegments === "number" && typeof availability.segmentCap === "number") {
@@ -139,15 +156,9 @@ export const explorationEffectsPlugin: GraphPlugin = {
                 description={row.description}
                 checked={effectsState[row.key]}
                 availability={
-                  availability?.[
-                    row.key === "pathPulseEnabled"
-                      ? "pathPulse"
-                      : row.key === "pathFlowEnabled"
-                        ? "pathFlow"
-                        : row.key === "lensEnabled"
-                          ? "lens"
-                          : "legend"
-                  ] ?? {
+                  (EFFECT_AVAILABILITY_KEYS[row.key] !== undefined
+                    ? availability?.[EFFECT_AVAILABILITY_KEYS[row.key]!]
+                    : undefined) ?? {
                     enabled: effectsState[row.key],
                     available: false,
                     reason: "Waiting for graph runtime",

explorer/src/workspaces/GraphWorkspace/plugins/explorationEffectsPluginPhaseC.tsx

@@ -47,6 +47,11 @@ const SCENE_EFFECT_ROWS: EffectRowConfig[] = [
     label: "Contours",
     description: "Low-contrast density halos around the strongest visible anchors.",
   },
+  {
+    key: "edgeLabelsEnabled",
+    label: "Edge Labels",
+    description: "Draw the relationship type on graph edges. Off restores label-free edges on dense graphs.",
+  },
   {
     key: "legendEnabled",
     label: "Regions Summary",
@@ -83,6 +88,7 @@ const AVAILABILITY_KEYS: Record<GraphEffectToggle, keyof GraphDiagnosticsSnapsho
   communitiesEnabled: "communities",
   centralityEnabled: "centrality",
   legendEnabled: "legend",
+  edgeLabelsEnabled: "edgeLabels",
   diagnosticsEnabled: "diagnostics",
 };
 

explorer/src/workspaces/GraphWorkspace/temporalLifecyclePredicates.ts

@@ -0,0 +1,31 @@
+import type { GraphLoadSummary } from "./types";
+
+/**
+ * Predicates for gating GraphWorkspace temporal API requests.
+ *
+ * Temporal bounds and snapshot requests must strictly not execute until the
+ * initial graph load has succeeded (summary !== undefined). An empty graph
+ * (nodeCount: 0) is still a successful load and must not be rejected.
+ */
+
+export function shouldFetchTemporalBounds(
+  summary: GraphLoadSummary | undefined,
+): boolean {
+  return summary !== undefined;
+}
+
+export function shouldFetchTemporalSnapshot({
+  debouncedTime,
+  isLoading,
+  summary,
+}: {
+  debouncedTime: Date | null;
+  isLoading: boolean;
+  summary: GraphLoadSummary | undefined;
+}): boolean {
+  return (
+    summary !== undefined &&
+    debouncedTime !== null &&
+    !isLoading
+  );
+}

explorer/src/workspaces/GraphWorkspace/temporalSnapshotGuards.ts

@@ -0,0 +1,113 @@
+/**
+ * Guards for the temporal snapshot fetch/apply lifecycle.
+ *
+ * The snapshot effect previously fetched /api/temporal/snapshot with no
+ * idempotency or ordering protection. Upstream churn (timeline recreation
+ * while bounds settle, play ticks resetting the playhead, drag events) could
+ * re-request the same `at` repeatedly, and responses could arrive after the
+ * scrubber had moved on.
+ *
+ * The guards enforce:
+ * - at most one in-flight request per scrubber position (identical `at`
+ *   values are deduplicated while a request is pending, breaking the
+ *   idle/play polling loop);
+ * - successful snapshots are cached per position and re-applied when the
+ *   scrubber returns (play wrap-around, back-scrubbing) without a refetch;
+ * - a response is applied only while the scrubber is still on its position,
+ *   so out-of-order responses cannot clobber a newer position's count;
+ * - failed, cancelled, or superseded requests release their position so it
+ *   can be fetched again on the next visit;
+ * - `reset()` drops all state when the underlying graph data is replaced
+ *   (reload/retry), because cached snapshots describe the previous graph.
+ *
+ * `createTemporalSnapshotGuards()` is stateful by design.
+ */
+
+export interface TemporalSnapshotResponse {
+  active_node_ids: string[];
+  active_node_count: number;
+}
+
+export interface TemporalSnapshotRequest {
+  /** null when the request was deduplicated because one is already in flight. */
+  seq: number | null;
+  /** The snapshot previously applied for this position, when revisiting it. */
+  cached: TemporalSnapshotResponse | null;
+}
+
+export interface TemporalSnapshotGuards {
+  /** Begin (or dedupe) a request for `atMs`; marks it as the current position. */
+  begin(atMs: number): TemporalSnapshotRequest;
+  /** True when the response for `atMs`/`seq` may be applied (scrubber still on `atMs`). */
+  shouldApply(atMs: number, seq: number): boolean;
+  /** Record a successful application and cache its snapshot for revisits. */
+  apply(atMs: number, seq: number, data: TemporalSnapshotResponse): void;
+  /** Release a position whose request failed, was cancelled, or was superseded. */
+  finish(atMs: number, seq: number): void;
+  /** Drop all state; call when the underlying graph data is replaced (reload). */
+  reset(): void;
+}
+
+interface SnapshotEntry {
+  seq: number;
+  /** null while the request is in flight (or before the first success). */
+  data: TemporalSnapshotResponse | null;
+}
+
+/** Upper bound on cached positions so long scrubbing sessions stay bounded. */
+const MAX_CACHED_POSITIONS = 256;
+
+export function createTemporalSnapshotGuards(): TemporalSnapshotGuards {
+  const entries = new Map<number, SnapshotEntry>();
+  let latestRequestSeq = 0;
+  let currentAtMs: number | null = null;
+
+  const evictOldest = () => {
+    while (entries.size > MAX_CACHED_POSITIONS) {
+      const oldestAtMs = entries.keys().next().value;
+      if (oldestAtMs === undefined) return;
+      entries.delete(oldestAtMs);
+    }
+  };
+
+  return {
+    begin(atMs) {
+      const existing = entries.get(atMs);
+      if (existing && existing.data === null) {
+        // Identical request already in flight: dedupe, but the scrubber is here now.
+        currentAtMs = atMs;
+        return { seq: null, cached: null };
+      }
+      latestRequestSeq += 1;
+      const seq = latestRequestSeq;
+      entries.set(atMs, { seq, data: existing?.data ?? null });
+      currentAtMs = atMs;
+      evictOldest();
+      return { seq, cached: existing?.data ?? null };
+    },
+
+    shouldApply(atMs, seq) {
+      return atMs === currentAtMs && entries.get(atMs)?.seq === seq;
+    },
+
+    apply(atMs, seq, data) {
+      const entry = entries.get(atMs);
+      if (entry && entry.seq === seq) {
+        entry.data = data;
+      }
+    },
+
+    finish(atMs, seq) {
+      const entry = entries.get(atMs);
+      if (entry && entry.seq === seq && entry.data === null) {
+        entries.delete(atMs);
+      }
+    },
+
+    reset() {
+      entries.clear();
+      latestRequestSeq = 0;
+      currentAtMs = null;
+    },
+  };
+}

explorer/src/workspaces/GraphWorkspace/types.ts

@@ -103,6 +103,7 @@ export type GraphEffectToggle =
   | "communitiesEnabled"
   | "centralityEnabled"
   | "legendEnabled"
+  | "edgeLabelsEnabled"
   | "diagnosticsEnabled";
 
 export interface GraphEffectsState {
@@ -113,6 +114,7 @@ export interface GraphEffectsState {
   semanticRegionsEnabled: boolean;
   contoursEnabled: boolean;
   pathfindingEnabled: boolean;
+  edgeLabelsEnabled: boolean;
   communitiesEnabled: boolean;
   centralityEnabled: boolean;
   legendEnabled: boolean;
@@ -186,6 +188,7 @@ export interface GraphDiagnosticsSnapshot {
     communities: GraphEffectAvailability;
     centrality: GraphEffectAvailability;
     legend: GraphEffectAvailability;
+    edgeLabels: GraphEffectAvailability;
     diagnostics: GraphEffectAvailability;
   };
 }

explorer/src/workspaces/GraphWorkspace/useGraphData.ts

@@ -1,223 +0,0 @@
-import { useQuery, useQueryClient } from "@tanstack/react-query";
-import { createGraphLoadProgress } from "./graphLoading";
-import type { ApiEdge, ApiNode, GraphDataSnapshot, GraphLoadProgress, GraphLayoutSource } from "./types";
-
-interface NodeListResponse {
-  nodes: ApiNode[];
-  total: number;
-  skip: number;
-  limit: number;
-  next_cursor?: string | null;
-}
-
-interface EdgeListResponse {
-  edges: ApiEdge[];
-  total: number;
-  skip: number;
-  limit: number;
-  next_cursor?: string | null;
-}
-
-const PAGE_LIMIT = 1000;
-
-async function fetchAllNodes(
-  signal: AbortSignal,
-  onProgress?: (progress: GraphLoadProgress) => void,
-): Promise<ApiNode[]> {
-  let cursor: string | null = null;
-  const collected: ApiNode[] = [];
-  let total: number | null = null;
-
-  while (true) {
-    const url = new URL("/api/graph/nodes", window.location.origin);
-    url.searchParams.set("limit", String(PAGE_LIMIT));
-    if (cursor) {
-      url.searchParams.set("cursor", cursor);
-    }
-
-    const response = await fetch(url.toString(), { signal });
-    if (!response.ok) {
-      throw new Error(`Fetch failed: ${response.status}`);
-    }
-
-    const data: NodeListResponse = await response.json();
-    if (!data.nodes?.length) {
-      break;
-    }
-
-    total = data.total ?? total;
-    collected.push(...data.nodes);
-    onProgress?.(createGraphLoadProgress({
-      phase: "fetching_nodes",
-      progressKind: total ? "determinate" : "indeterminate",
-      loaded: collected.length,
-      total,
-      nodesLoaded: collected.length,
-      nodesTotal: total,
-      edgesLoaded: 0,
-      edgesTotal: null,
-      message: total
-        ? `Loading nodes ${collected.length.toLocaleString()} of ${total.toLocaleString()}`
-        : `Loading nodes ${collected.length.toLocaleString()}`,
-    }));
-
-    if (!data.next_cursor) {
-      break;
-    }
-    cursor = data.next_cursor;
-    await yieldToMain();
-  }
-
-  return collected;
-}
-
-async function fetchAllEdges(
-  signal: AbortSignal,
-  nodeIds: Set<string>,
-  nodeProgress: { loaded: number; total: number | null },
-  onProgress?: (progress: GraphLoadProgress) => void,
-): Promise<ApiEdge[]> {
-  let cursor: string | null = null;
-  const collected: ApiEdge[] = [];
-  const seenEdgeIds = new Set<string>();
-  let total: number | null = null;
-  let warnedOverTotal = false;
-
-  while (true) {
-    const url = new URL("/api/graph/edges", window.location.origin);
-    url.searchParams.set("limit", String(PAGE_LIMIT));
-    if (cursor) {
-      url.searchParams.set("cursor", cursor);
-    }
-
-    const response = await fetch(url.toString(), { signal });
-    if (!response.ok) {
-      throw new Error(`Fetch failed: ${response.status}`);
-    }
-
-    const data: EdgeListResponse = await response.json();
-    if (!data.edges?.length) {
-      break;
-    }
-
-    total = data.total ?? total;
-    const validEdges = data.edges.filter((edge) => {
-      if (!nodeIds.has(edge.source) || !nodeIds.has(edge.target)) {
-        return false;
-      }
-      if (seenEdgeIds.has(edge.id)) {
-        return false;
-      }
-      seenEdgeIds.add(edge.id);
-      return true;
-    });
-    collected.push(...validEdges);
-    const safeLoaded = total ? Math.min(seenEdgeIds.size, total) : seenEdgeIds.size;
-    if (!warnedOverTotal && total !== null && seenEdgeIds.size > total) {
-      warnedOverTotal = true;
-      console.warn("[graph-runtime] edge pagination returned more unique edge ids than total", {
-        uniqueEdgesLoaded: seenEdgeIds.size,
-        total,
-      });
-    }
-    onProgress?.(createGraphLoadProgress({
-      phase: "fetching_edges",
-      progressKind: total ? "determinate" : "indeterminate",
-      loaded: safeLoaded,
-      total,
-      nodesLoaded: nodeProgress.loaded,
-      nodesTotal: nodeProgress.total,
-      edgesLoaded: safeLoaded,
-      edgesTotal: total,
-      message: total
-        ? `Loading edges ${safeLoaded.toLocaleString()} of ${total.toLocaleString()}`
-        : `Loading edges ${safeLoaded.toLocaleString()}`,
-    }));
-
-    if (!data.next_cursor) {
-      break;
-    }
-    cursor = data.next_cursor;
-    await yieldToMain();
-  }
-
-  return collected;
-}
-
-function yieldToMain(): Promise<void> {
-  if ("scheduler" in window && typeof (window as Window & { scheduler?: { yield?: () => Promise<void> } }).scheduler?.yield === "function") {
-    return (window as Window & { scheduler: { yield: () => Promise<void> } }).scheduler.yield();
-  }
-  return new Promise((resolve) => setTimeout(resolve, 0));
-}
-
-function hasUsableCoordinate(value: number | null | undefined): value is number {
-  return typeof value === "number" && Number.isFinite(value);
-}
-
-interface UseGraphDataOptions {
-  enabled?: boolean;
-  onProgress?: (progress: GraphLoadProgress) => void;
-}
-
-export function useGraphData(options: UseGraphDataOptions = {}) {
-  const { enabled = true, onProgress } = options;
-
-  return useQuery<GraphDataSnapshot>({
-    queryKey: ["graph", "runtime-snapshot"],
-    enabled,
-    staleTime: Infinity,
-    queryFn: async ({ signal }): Promise<GraphDataSnapshot> => {
-      const startedAt = performance.now();
-      onProgress?.(createGraphLoadProgress({
-        phase: "bootstrapping",
-        progressKind: "indeterminate",
-        nodesLoaded: 0,
-        nodesTotal: null,
-        edgesLoaded: 0,
-        edgesTotal: null,
-        message: "Preparing graph session",
-      }));
-
-      const nodes = await fetchAllNodes(signal, onProgress);
-      const nodeIds = new Set(nodes.map((node) => node.id));
-      const edges = await fetchAllEdges(
-        signal,
-        nodeIds,
-        { loaded: nodes.length, total: nodes.length },
-        onProgress,
-      );
-
-      onProgress?.(createGraphLoadProgress({
-        phase: "hydrating_scene",
-        progressKind: "indeterminate",
-        nodesLoaded: nodes.length,
-        nodesTotal: nodes.length,
-        edgesLoaded: edges.length,
-        edgesTotal: edges.length,
-        message: "Preparing graph runtime snapshot",
-      }));
-
-      return {
-        nodes,
-        edges,
-        summary: {
-          nodeCount: nodes.length,
-          edgeCount: edges.length,
-          loadTimeMs: Math.round(performance.now() - startedAt),
-          hasCoordinates: nodes.some((node) => hasUsableCoordinate(node.x) && hasUsableCoordinate(node.y)),
-          layoutSource: (nodes.some((node) => hasUsableCoordinate(node.x) && hasUsableCoordinate(node.y))
-            ? "provided"
-            : "runtime") as GraphLayoutSource,
-          layoutReady: nodes.some((node) => hasUsableCoordinate(node.x) && hasUsableCoordinate(node.y)),
-        },
-        fetchedAt: Date.now(),
-      };
-    },
-  });
-}
-
-export function useReloadGraphData() {
-  const queryClient = useQueryClient();
-  return () => queryClient.invalidateQueries({ queryKey: ["graph", "runtime-snapshot"] });
-}

explorer/tests/graphSceneState.display.test.ts

@@ -1061,3 +1061,198 @@ test("checkGroupedViewAvailability returns available when communities exist", ()
   assert.equal(result.reason, null);
 });
 
+
+// ── #1009: edge label data-path regression tests ─────────────────────────────
+
+test("resolveDisplayGraph parallel-bundle preserves edgeType on aggregated edge", () => {
+  addNode("a");
+  addNode("b");
+  batchMergeEdges([
+    { id: "e1", source: "a", target: "b", attributes: { edgeType: "causes", weight: 1, properties: {} } },
+    { id: "e2", source: "a", target: "b", attributes: { edgeType: "causes", weight: 2, properties: {} } },
+  ]);
+
+  const { graph: displayGraph } = resolveDisplayGraph("", [], [], "full", { aggregationEnabled: true });
+  assert.equal(displayGraph.size, 1);
+
+  const edgeId = displayGraph.edges()[0];
+  const attrs = displayGraph.getEdgeAttributes(edgeId) as { edgeType?: string; isAggregated?: boolean };
+  assert.equal(attrs.isAggregated, true);
+  // The aggregated representative must carry the relationship text through to
+  // the edgeReducer's label assignment.
+  assert.equal(typeof attrs.edgeType, "string");
+  assert.ok((attrs.edgeType ?? "").length > 0, "aggregated edge must have a non-empty edgeType");
+});
+
+test("resolveDisplayGraph parallel-bundle picks dominant edgeType across mixed types", () => {
+  addNode("a");
+  addNode("b");
+  batchMergeEdges([
+    { id: "e1", source: "a", target: "b", attributes: { edgeType: "inhibits", weight: 1, properties: {} } },
+    { id: "e2", source: "a", target: "b", attributes: { edgeType: "inhibits", weight: 1, properties: {} } },
+    { id: "e3", source: "a", target: "b", attributes: { edgeType: "activates", weight: 1, properties: {} } },
+  ]);
+
+  const { graph: displayGraph } = resolveDisplayGraph("", [], [], "full", { aggregationEnabled: true });
+  const edgeId = displayGraph.edges()[0];
+  const attrs = displayGraph.getEdgeAttributes(edgeId) as { edgeType?: string; dominantEdgeType?: string };
+  // "inhibits" appears twice so it must be the dominant type.
+  assert.equal(attrs.edgeType, "inhibits");
+  assert.equal(attrs.dominantEdgeType, "inhibits");
+});
+
+test("resolveDisplayGraph grouped view community edges carry non-empty edgeType", () => {
+  const left = ["g1", "g2", "g3", "g4"];
+  const right = ["h1", "h2", "h3", "h4"];
+  [...left, ...right].forEach((nodeId, index) => addNode(nodeId, index < left.length ? "left" : "right"));
+
+  let edgeIndex = 0;
+  for (let i = 0; i < left.length; i += 1) {
+    for (let j = 0; j < left.length; j += 1) {
+      if (i !== j) {
+        batchMergeEdges([{
+          id: `lg-${edgeIndex++}`,
+          source: left[i],
+          target: left[j],
+          attributes: { edgeType: "co_occurs", weight: 3, properties: {} },
+        }]);
+      }
+    }
+  }
+  for (let i = 0; i < right.length; i += 1) {
+    for (let j = 0; j < right.length; j += 1) {
+      if (i !== j) {
+        batchMergeEdges([{
+          id: `rg-${edgeIndex++}`,
+          source: right[i],
+          target: right[j],
+          attributes: { edgeType: "co_occurs", weight: 3, properties: {} },
+        }]);
+      }
+    }
+  }
+  batchMergeEdges([{ id: "bridge-g", source: "g1", target: "h1", attributes: { edgeType: "interacts_with", weight: 0.1, properties: {} } }]);
+
+  const { graph: displayGraph, state } = resolveDisplayGraph("", [], [], "grouped", { aggregationEnabled: true });
+  assert.equal(state.groupedViewAvailable, true);
+
+  const communityEdges = displayGraph.edges().filter((edgeId) => {
+    const attrs = displayGraph.getEdgeAttributes(edgeId) as { bundleKind?: string };
+    return attrs.bundleKind === "community";
+  });
+  assert.ok(communityEdges.length > 0, "expected at least one community bundle edge");
+
+  for (const edgeId of communityEdges) {
+    const attrs = displayGraph.getEdgeAttributes(edgeId) as { edgeType?: string };
+    assert.equal(typeof attrs.edgeType, "string");
+    assert.ok((attrs.edgeType ?? "").length > 0, `community edge ${edgeId} must have a non-empty edgeType`);
+  }
+});
+
+test("resolveDisplayGraph raw edge preserves exact edgeType string for label rendering", () => {
+  addNode("src");
+  addNode("tgt");
+  batchMergeEdges([{
+    id: "raw-1",
+    source: "src",
+    target: "tgt",
+    attributes: { edgeType: "works_for", weight: 1, properties: {} },
+  }]);
+
+  // In full view without aggregation the edge passes through unchanged.
+  const { graph: displayGraph } = resolveDisplayGraph("", [], [], "full", { aggregationEnabled: false });
+  assert.equal(displayGraph.size, 1);
+
+  const edgeId = displayGraph.edges()[0];
+  const attrs = displayGraph.getEdgeAttributes(edgeId) as { edgeType?: string };
+  assert.equal(attrs.edgeType, "works_for");
+});
+
+test("resolveDisplayGraph does not produce empty-string edgeType on aggregated edges when source has empty type", () => {
+  addNode("a");
+  addNode("b");
+  // Simulate an API response where type is empty string — the aggregation
+  // path must not propagate a blank label.
+  batchMergeEdges([
+    { id: "e-empty-1", source: "a", target: "b", attributes: { edgeType: "", weight: 1, properties: {} } },
+    { id: "e-empty-2", source: "a", target: "b", attributes: { edgeType: "", weight: 1, properties: {} } },
+  ]);
+
+  const { graph: displayGraph } = resolveDisplayGraph("", [], [], "full", { aggregationEnabled: true });
+  const edgeId = displayGraph.edges()[0];
+  const attrs = displayGraph.getEdgeAttributes(edgeId) as {
+    edgeType?: string;
+    isAggregated?: boolean;
+  };
+  assert.equal(attrs.isAggregated, true);
+  // The aggregation falls back to "related_to" when all source edgeTypes are
+  // empty, so the rendered label should never be an empty string.
+  assert.equal(attrs.edgeType, "related_to");
+});
+
+test("resolveEdgeElementStyle hidden class produces hidden:true for suppressed edges", () => {
+  // Verify the data condition the edgeReducer relies on: hidden-classified
+  // edges must have hidden:true so that the label assignment sets undefined.
+  const style = resolveEdgeElementStyle(
+    GRAPH_THEME,
+    "overview",
+    "inactive",
+    {
+      edgeType: "causes",
+      weight: 1,
+      properties: {},
+      edgeVariant: "line",
+      visualPriority: 0.05,
+      baseSize: 0.3,
+    },
+    "source",
+    "target",
+    "full",
+    "inactive-edge",
+    "hidden",
+  );
+  assert.equal(style.hidden, true);
+});
+
+// ── #1009 maintainer-blocking regression: single-edge empty edgeType ─────────
+
+test("resolveDisplayGraph single-edge normalizes empty-string edgeType to related_to", () => {
+  addNode("a");
+  addNode("b");
+  // One edge only — exercises the entries.length === 1 path in aggregateDisplayGraph.
+  batchMergeEdges([{
+    id: "e-single-empty",
+    source: "a",
+    target: "b",
+    attributes: { edgeType: "", weight: 1, properties: {} },
+  }]);
+
+  const { graph: displayGraph } = resolveDisplayGraph("", [], [], "full", { aggregationEnabled: true });
+  assert.equal(displayGraph.size, 1);
+
+  const edgeId = displayGraph.edges()[0];
+  const attrs = displayGraph.getEdgeAttributes(edgeId) as { edgeType?: string; dominantEdgeType?: string };
+  assert.equal(attrs.edgeType, "related_to",
+    "single-edge path must normalize empty edgeType to the canonical fallback");
+  assert.equal(attrs.dominantEdgeType, "related_to",
+    "single-edge dominantEdgeType must also be normalized");
+});
+
+test("resolveDisplayGraph single-edge preserves a valid non-empty edgeType unchanged", () => {
+  addNode("a");
+  addNode("b");
+  batchMergeEdges([{
+    id: "e-single-valid",
+    source: "a",
+    target: "b",
+    attributes: { edgeType: "works_for", weight: 1, properties: {} },
+  }]);
+
+  const { graph: displayGraph } = resolveDisplayGraph("", [], [], "full", { aggregationEnabled: true });
+  assert.equal(displayGraph.size, 1);
+
+  const edgeId = displayGraph.edges()[0];
+  const attrs = displayGraph.getEdgeAttributes(edgeId) as { edgeType?: string };
+  assert.equal(attrs.edgeType, "works_for",
+    "single-edge path must not alter a valid relationship type");
+});

explorer/tests/markdownContentViewer.test.ts

@@ -0,0 +1,265 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import React from "react";
+import { renderToString } from "react-dom/server";
+
+(globalThis as any).React = React;
+
+import { MarkdownContentViewer } from "../src/workspaces/GraphWorkspace/MarkdownContentViewer.tsx";
+import { isSafeUrl } from "../src/workspaces/GraphWorkspace/markdownUrlSafety.ts";
+
+test("isSafeUrl permits safe http, https, and mailto URLs and relative paths", () => {
+  assert.equal(isSafeUrl("https://example.com"), true);
+  assert.equal(isSafeUrl("http://localhost:8000"), true);
+  assert.equal(isSafeUrl("mailto:user@example.com"), true);
+  assert.equal(isSafeUrl("#section-1"), true);
+  assert.equal(isSafeUrl("/relative/path"), true);
+});
+
+test("isSafeUrl rejects protocol-relative URLs and dangerous schemes", () => {
+  // Protocol-relative URLs (must be blocked)
+  assert.equal(isSafeUrl("//evil.com"), false);
+  assert.equal(isSafeUrl("//localhost:8000"), false);
+  assert.equal(isSafeUrl("//"), false);
+
+  // Dangerous schemes
+  assert.equal(isSafeUrl("javascript:alert('xss')"), false);
+  assert.equal(isSafeUrl("JAVASCRIPT:alert(1)"), false);
+  assert.equal(isSafeUrl("data:text/html;base64,PHNjcmlwdD4="), false);
+  assert.equal(isSafeUrl("vbscript:MsgBox(1)"), false);
+  assert.equal(isSafeUrl(""), false);
+  assert.equal(isSafeUrl(undefined), false);
+});
+
+// ─── C URL contract: whitespace-only strings ────────────────────────────────
+// The CommonMark parser normalises whitespace-only link destinations to "" so
+// these values are unreachable through normal markdown rendering. However, the
+// function is exported and its direct-call contract must be correct.
+test("isSafeUrl rejects whitespace-only strings (contract correctness)", () => {
+  assert.equal(isSafeUrl(" "), false, "single space must be rejected");
+  assert.equal(isSafeUrl("\t"), false, "tab must be rejected");
+  assert.equal(isSafeUrl("\n"), false, "newline must be rejected");
+  assert.equal(isSafeUrl("   "), false, "multiple spaces must be rejected");
+  assert.equal(isSafeUrl(" \t\n "), false, "mixed whitespace must be rejected");
+});
+
+test("renders Preview mode with formatted Markdown elements and tabs", () => {
+  const markdown = `# Main Title\n\n**Bold Statement**\n\n* Item A\n* Item B`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content: markdown, defaultMode: "preview" }));
+
+  // Tab buttons are present
+  assert.equal(html.includes("Preview"), true);
+  assert.equal(html.includes("Source"), true);
+  assert.equal(html.includes("Copy"), true);
+
+  // Formatted preview elements
+  assert.equal(html.includes("Main Title"), true);
+  assert.equal(html.includes("Bold Statement"), true);
+  assert.equal(html.includes("<strong>Bold Statement</strong>"), true);
+  assert.equal(html.includes("Item A"), true);
+  assert.equal(html.includes("Item B"), true);
+});
+
+test("renders Source mode with exact unmodified text inside pre/code", () => {
+  const markdown = `# Title 🚀\n\n  * Indented item\n\n\`\`\`python\ndef test():\n    return "α + β"\n\`\`\``;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content: markdown, defaultMode: "source" }));
+
+  assert.equal(html.includes("<pre"), true);
+  assert.equal(html.includes("<code"), true);
+  assert.equal(html.includes("# Title 🚀"), true);
+  assert.equal(html.includes("  * Indented item"), true);
+  assert.equal(html.includes('return &quot;α + β&quot;'), true);
+});
+
+test("renders raw HTML safely as escaped text without executing elements", () => {
+  const dangerousHtml = `<script>alert("XSS")</script><iframe src="https://evil.com"></iframe>`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content: dangerousHtml, defaultMode: "preview" }));
+
+  // Script and iframe tags must NOT be rendered as active DOM tags
+  assert.equal(html.includes("<script>"), false);
+  assert.equal(html.includes("<iframe"), false);
+  // Content is escaped as text
+  assert.equal(html.includes("&lt;script&gt;"), true);
+});
+
+// ─── C-1: HAST node prop must not reach the DOM ─────────────────────────────
+// react-markdown passes a HAST `node` (Element) object to custom component
+// overrides. Before this fix, ...props spread caused React 19 to serialise it
+// as node="[object Object]" on every <a> and <code> element.
+test("rendered links do not expose the HAST node object as a DOM attribute", () => {
+  const content = `[Example](https://example.com)\n\nInline \`code\` here.`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content, defaultMode: "preview" }));
+
+  // The rendered HTML must not contain the serialised HAST object
+  assert.equal(html.includes("node="), false, "node= attribute must not appear in rendered HTML");
+  assert.equal(html.includes("[object Object]"), false, "serialised HAST object must not appear in rendered HTML");
+
+  // The link must still render correctly with the right href
+  assert.equal(html.includes('href="https://example.com"'), true, "href must be present");
+});
+
+// ─── C-2: Fragment links must not open in a new tab ─────────────────────────
+// Links to in-document anchors such as #section or GFM footnote backlinks like
+// #user-content-fn-1 must stay in the current document. Only external links
+// use target="_blank".
+test("fragment links render in the current document without target blank", () => {
+  const content = `[Jump to section](#introduction)\n\n[External](https://example.com)`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content, defaultMode: "preview" }));
+
+  // Fragment link must have the href
+  assert.equal(html.includes('href="#introduction"'), true, "fragment href must be present");
+
+  // Confirm no target=_blank attribute appears anywhere near the fragment link.
+  // We check that the output contains a fragment href WITHOUT target="_blank"
+  // by verifying the two strings are not both present (the external link has
+  // target blank; the fragment link must not).
+  const fragmentLinkIdx = html.indexOf('href="#introduction"');
+  assert.notEqual(fragmentLinkIdx, -1, "fragment link must be rendered");
+  // Inspect the 80 chars around the fragment href — should not contain target
+  const fragmentContext = html.slice(Math.max(0, fragmentLinkIdx - 10), fragmentLinkIdx + 90);
+  assert.equal(fragmentContext.includes('target="_blank"'), false, "fragment link must not have target=_blank");
+
+  // External link must still have target blank
+  assert.equal(html.includes('href="https://example.com"'), true, "external href must be present");
+  assert.equal(html.includes('target="_blank"'), true, "external link must have target=_blank");
+  assert.equal(html.includes('rel="noopener noreferrer"'), true, "external link must have rel");
+});
+
+test("GFM footnote backlinks render without target blank", () => {
+  // GFM footnote syntax: footnote ref in text + definition below
+  const content = `See the note[^1] for more.\n\n[^1]: This is the footnote text.`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content, defaultMode: "preview" }));
+
+  // The footnote reference link (#user-content-fn-1) and backlink
+  // (#user-content-fnref-1) are fragment links and must not open in a new tab.
+  // We verify no fragment href is paired with target=_blank.
+  // Extract all href="#..." occurrences and confirm none is adjacent to target=_blank.
+  const anchorMatches = [...html.matchAll(/href="#[^"]*"/g)];
+  assert.ok(anchorMatches.length > 0, "GFM footnotes must produce fragment links");
+  for (const match of anchorMatches) {
+    const start = match.index ?? 0;
+    const context = html.slice(Math.max(0, start - 10), start + 120);
+    assert.equal(
+      context.includes('target="_blank"'),
+      false,
+      `fragment link ${match[0]} must not have target=_blank`,
+    );
+  }
+});
+
+// ─── C-1-R: GFM footnote attributes must be preserved (regression test) ─────
+// The C-1 fix (removing the HAST `node` prop) must NOT silently drop other
+// legitimate HAST attributes. remark-gfm generates the following on footnote
+// links that are required for correct in-page navigation and accessibility:
+//
+//   Footnote reference anchor:
+//     id="user-content-fnref-1"           ← backlink target
+//     data-footnote-ref="true"
+//     aria-describedby="footnote-label"
+//
+//   Footnote back-link anchor:
+//     data-footnote-backref=""
+//     aria-label="Back to reference 1"    ← screen-reader label
+//     class="data-footnote-backref"
+//
+// If these are absent, clicking the ↩ back-link cannot scroll back to the
+// in-text reference, and screen readers cannot announce the backlink purpose.
+test("GFM footnote links preserve generated id, aria, and class attributes", () => {
+  const content = `See the note[^1] for more.\n\n[^1]: This is the footnote text.`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content, defaultMode: "preview" }));
+
+  // The HAST `node` object must not appear serialised as a DOM attribute.
+  assert.equal(html.includes("node="), false, "node= attribute must not appear in HTML");
+  assert.equal(html.includes("[object Object]"), false, "serialised HAST object must not appear in HTML");
+
+  // Footnote reference anchor must retain its id so the backlink can navigate to it.
+  assert.equal(
+    html.includes('id="user-content-fnref-1"'),
+    true,
+    "footnote reference anchor must retain id for back-navigation",
+  );
+
+  // Footnote backlink must retain its aria-label for screen-reader accessibility.
+  assert.equal(
+    html.includes('aria-label="Back to reference 1"'),
+    true,
+    "footnote backlink must retain aria-label for accessibility",
+  );
+
+  // Footnote backlink must retain its class attribute.
+  assert.equal(
+    html.includes('class="data-footnote-backref"'),
+    true,
+    "footnote backlink must retain class attribute",
+  );
+});
+
+test("renders safe links as <a> with target blank and unclickable span for unsafe links", () => {
+  const content = `[Safe Link](https://getsemantica.ai)\n\n[Unsafe Scheme](javascript:alert(1))\n\n[Protocol Relative](//evil.com)`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content, defaultMode: "preview" }));
+
+  // Safe link renders as <a> with security attributes
+  assert.equal(html.includes('href="https://getsemantica.ai"'), true);
+  assert.equal(html.includes('target="_blank"'), true);
+  assert.equal(html.includes('rel="noopener noreferrer"'), true);
+
+  // Unsafe links do NOT render as <a> tags
+  assert.equal(html.includes('href="javascript:alert(1)"'), false);
+  assert.equal(html.includes('href="//evil.com"'), false);
+  assert.equal(html.includes("Unsafe Scheme"), true);
+  assert.equal(html.includes("Protocol Relative"), true);
+});
+
+test("renders remote images as safe placeholder badges instead of <img> tags", () => {
+  const content = `![System Diagram](https://example.com/diagram.png)`;
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content, defaultMode: "preview" }));
+
+  // No <img> tag rendered
+  assert.equal(html.includes("<img"), false);
+  // Image placeholder badge rendered
+  assert.equal(html.includes("Image:"), true);
+  assert.equal(html.includes("System Diagram"), true);
+});
+
+test("renders clear empty-state message when content is empty or null", () => {
+  const emptyHtml = renderToString(React.createElement(MarkdownContentViewer, { content: "" }));
+  assert.equal(emptyHtml.includes("No content available for this node."), true);
+
+  const nullHtml = renderToString(React.createElement(MarkdownContentViewer, { content: null }));
+  assert.equal(nullHtml.includes("No content available for this node."), true);
+});
+
+test("renders plain text cleanly without requiring Markdown formatting", () => {
+  const plainText = "Plain entity summary text without markdown formatting.";
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content: plainText, defaultMode: "preview" }));
+
+  assert.equal(html.includes(plainText), true);
+});
+
+test("handles very large Markdown content without failure", () => {
+  const largeContent = `# Large Knowledge Node\n\n` + "Structured observation paragraph. ".repeat(400);
+  assert.equal(largeContent.length > 10000, true);
+
+  const html = renderToString(React.createElement(MarkdownContentViewer, { content: largeContent, defaultMode: "preview" }));
+  assert.equal(html.includes("Large Knowledge Node"), true);
+});
+
+// ─── H-2: Stale copied state lifecycle (SSR-compatible portion) ─────────────
+// Full state-transition testing (Node A → copy → Node B) requires an interactive
+// framework. The lifecycle correctness is guaranteed by the render-phase
+// previous-prop synchronisation pattern: a `copiedForContent` state value tracks
+// the content for which the copied indicator was set; when `content` changes, the
+// mismatch is detected during render and `copied` is reset to false in the same
+// React batch, before the new node's UI is painted. What we CAN verify in SSR
+// is that the initial render for any content value shows the Copy button (not the
+// Copied indicator), which confirms the initial state is always clean.
+test("copy button always starts in un-copied state on initial render", () => {
+  const html = renderToString(React.createElement(MarkdownContentViewer, {
+    content: "# Some Node\n\nDescription text.",
+    defaultMode: "preview",
+  }));
+
+  // Initial render must show 'Copy', never 'Copied'
+  assert.equal(html.includes("Copy"), true, "Copy button must be present on initial render");
+  assert.equal(html.includes("Copied"), false, "Copied indicator must NOT be present on initial render");
+});

explorer/tests/temporalLifecycle.test.ts

@@ -0,0 +1,114 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+
+import {
+  shouldFetchTemporalBounds,
+  shouldFetchTemporalSnapshot,
+} from "../src/workspaces/GraphWorkspace/temporalLifecyclePredicates.ts";
+import type { GraphLoadSummary } from "../src/workspaces/GraphWorkspace/types.ts";
+
+const sampleSummary: GraphLoadSummary = {
+  nodeCount: 42,
+  edgeCount: 78,
+  loadTimeMs: 120,
+  hasCoordinates: true,
+  layoutSource: "provided",
+  layoutReady: true,
+};
+
+const emptyGraphSummary: GraphLoadSummary = {
+  nodeCount: 0,
+  edgeCount: 0,
+  loadTimeMs: 15,
+  hasCoordinates: false,
+  layoutSource: "runtime",
+  layoutReady: false,
+};
+
+// ── shouldFetchTemporalBounds ────────────────────────────────────────────────
+
+test("temporal bounds: false when summary is undefined (initial mount or failed load)", () => {
+  assert.equal(
+    shouldFetchTemporalBounds(undefined),
+    false,
+    "bounds request must not run before graph load succeeds",
+  );
+});
+
+test("temporal bounds: true when non-empty summary is present", () => {
+  assert.equal(
+    shouldFetchTemporalBounds(sampleSummary),
+    true,
+    "bounds request should run when successful graph summary exists",
+  );
+});
+
+test("temporal bounds: true when successful summary has nodeCount of 0", () => {
+  assert.equal(
+    shouldFetchTemporalBounds(emptyGraphSummary),
+    true,
+    "an empty graph is still a successful load and must allow bounds fetching",
+  );
+});
+
+// ── shouldFetchTemporalSnapshot ──────────────────────────────────────────────
+
+test("temporal snapshot: false when summary is undefined even if scrubber time is set and isLoading is false", () => {
+  assert.equal(
+    shouldFetchTemporalSnapshot({
+      debouncedTime: new Date("2024-01-01T00:00:00Z"),
+      isLoading: false,
+      summary: undefined,
+    }),
+    false,
+    "snapshot request must not run when graph load failed",
+  );
+});
+
+test("temporal snapshot: false when graph is currently loading", () => {
+  assert.equal(
+    shouldFetchTemporalSnapshot({
+      debouncedTime: new Date("2024-01-01T00:00:00Z"),
+      isLoading: true,
+      summary: sampleSummary,
+    }),
+    false,
+    "snapshot request must not run while graph is loading",
+  );
+});
+
+test("temporal snapshot: false when debouncedTime is null", () => {
+  assert.equal(
+    shouldFetchTemporalSnapshot({
+      debouncedTime: null,
+      isLoading: false,
+      summary: sampleSummary,
+    }),
+    false,
+    "snapshot request must not run without a scrubber timestamp",
+  );
+});
+
+test("temporal snapshot: true when summary exists, isLoading is false, and time is set", () => {
+  assert.equal(
+    shouldFetchTemporalSnapshot({
+      debouncedTime: new Date("2024-01-01T00:00:00Z"),
+      isLoading: false,
+      summary: sampleSummary,
+    }),
+    true,
+    "snapshot request should run after graph load succeeds and time is set",
+  );
+});
+
+test("temporal snapshot: true when successful summary has 0 nodes, isLoading is false, and time is set", () => {
+  assert.equal(
+    shouldFetchTemporalSnapshot({
+      debouncedTime: new Date("2024-01-01T00:00:00Z"),
+      isLoading: false,
+      summary: emptyGraphSummary,
+    }),
+    true,
+    "empty successful graph must allow snapshot requests once ready",
+  );
+});