Merge branch 'main' into fix/py39-install-deps

fix(deps): unblock python 3.9 core install
2026-09-04 04:01:07 +00:00 · 2026-09-03 22:43:31 +05:30 · 2026-09-03 21:48:07 +05:00
56 changed files with 258 additions and 6161 deletions
@@ -1461,22 +1461,6 @@ semantica-explorer --graph my_graph.json

 For contributor / dev-server setup: **[explorer/README.md: Local Setup Guide](explorer/README.md)**

-The CLI exposes the loaded `ContextGraph`. To also browse and edit an existing
-`AgentMemory`, create the ASGI app programmatically with both live objects:
-
-```python
-from semantica.context import AgentMemory, ContextGraph
-from semantica.explorer.app import create_app
-from semantica.explorer.session import GraphSession
-
-graph = ContextGraph()
-memory = AgentMemory()
-app = create_app(session=GraphSession(graph), agent_memory=memory)
-```
-
-The Memories workspace is shown only when `agent_memory` is provided. Apply
-updates the supplied runtime object; it does not add disk persistence.
-
 ---

 ## What's New in v0.6.7
@@ -1485,7 +1469,7 @@ updates the supplied runtime object; it does not add disk persistence.

 - **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 Explorer can validate and apply Markdown edits to individual graph nodes and AgentMemory items supplied by the hosting application
+- **`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
@@ -195,7 +195,7 @@ apt29_intel = context.retrieve(
 ```python
 from semantica.llms import LiteLLM

-llm = LiteLLM(model="anthropic/claude-sonnet-5")
+llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")

 result = context.query_with_reasoning(
    "What are APT29's known TTPs against healthcare infrastructure, "
@@ -281,7 +281,7 @@ context.store(
    link_entities=True,
 )

-llm    = LiteLLM(model="anthropic/claude-sonnet-5")
+llm    = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
 result = context.query_with_reasoning(
    "Trace the C2 infrastructure chain for APT29 operations targeting "
    "ITAR-controlled contractors in 2025. Include IP ranges, ASNs, and TTPs.",
@@ -351,7 +351,7 @@ Parent: wmiprvse.exe
 Sigma match: T1053.005 Scheduled Task/Job
 """

-llm    = LiteLLM(model="anthropic/claude-sonnet-5")
+llm    = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
 triage = soc_context.query_with_reasoning(
    "Triage this SIEM alert and identify the correct response runbook:\n{}".format(alert_text),
    llm_provider=llm,
@@ -425,7 +425,7 @@ Patient: 68F, AF, CKD stage 3b (eGFR 32). On warfarin (INR target 2.0–3.0).
 Presenting for elective hip replacement. Concurrent: amiodarone 200mg, atorvastatin 40mg.
 """

-llm    = LiteLLM(model="anthropic/claude-sonnet-5")
+llm    = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
 answer = clinical_context.query_with_reasoning(
    "What is the evidence-based warfarin bridging protocol for this patient "
    "given CKD and amiodarone interaction risk?\n\n{}".format(patient_context),
@@ -495,7 +495,7 @@ compliance_context.store(
    extract_relationships=True,
 )

-llm    = LiteLLM(model="anthropic/claude-sonnet-5")
+llm    = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
 answer = compliance_context.query_with_reasoning(
    "Under Basel III CRE20, what are the RWA calculation requirements for "
    "commercial real estate exposures with LTV > 80%? "
@@ -275,20 +275,20 @@ print(data)

 **LiteLLM** is a universal adapter that provides a single interface to over 100 different LLM providers, including Anthropic Claude, Azure OpenAI, AWS Bedrock, Google Vertex AI, and local Ollama instances. It acts as a translation layer, converting your unified API calls into provider-specific requests, enabling easy switching between providers without code changes.

-`LiteLLM` is the Swiss Army knife. It wraps the `litellm` library, which speaks to every major provider using a unified completion API. The model string encodes both provider and model name: `"anthropic/claude-sonnet-5"`, `"azure/gpt-4o"`, `"bedrock/anthropic.claude-sonnet-4-5-20250929-v1:0"`, `"ollama/llama3.2"`. Change the string, change the provider — no other code changes needed.
+`LiteLLM` is the Swiss Army knife. It wraps the `litellm` library, which speaks to every major provider using a unified completion API. The model string encodes both provider and model name: `"anthropic/claude-sonnet-4-20250514"`, `"azure/gpt-4o"`, `"bedrock/anthropic.claude-3-5-sonnet-20241022-v2:0"`, `"ollama/llama3.2"`. Change the string, change the provider — no other code changes needed.

 ```python
 from semantica.llms import LiteLLM

 # Anthropic Claude — highest accuracy for complex reasoning
-llm = LiteLLM(model="anthropic/claude-sonnet-5")
+llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
 # Reads ANTHROPIC_API_KEY from environment

 # Azure OpenAI — compliance and data-residency requirements
 llm = LiteLLM(model="azure/gpt-4o", api_key="YOUR_AZURE_KEY")

 # AWS Bedrock — existing cloud agreement, no new vendor
-llm = LiteLLM(model="bedrock/anthropic.claude-sonnet-4-5-20250929-v1:0")
+llm = LiteLLM(model="bedrock/anthropic.claude-3-5-sonnet-20241022-v2:0")

 # Google Vertex AI
 llm = LiteLLM(model="vertex_ai/gemini-1.5-pro")
@@ -306,7 +306,7 @@ The environment-variable convention for each provider: `ANTHROPIC_API_KEY`, `AZU
 import os

 PROVIDER_MAP = {
-    "prod":    "anthropic/claude-sonnet-5",
+    "prod":    "anthropic/claude-sonnet-4-20250514",
    "staging": "openai/gpt-4o-mini",
    "local":   "ollama/llama3.2",
    "azure":   "azure/gpt-4o",
@@ -378,7 +378,7 @@ print("FAST: {}  (conf={:.0%})".format(fast_result["response"], fast_result["con

 # Tier 2: deep answer with Claude if confidence is below threshold
 if fast_result["confidence"] < 0.85:
-    deep_llm = LiteLLM(model="anthropic/claude-sonnet-5")
+    deep_llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
    deep_result = context.query_with_reasoning(
        query, llm_provider=deep_llm, max_results=15, max_hops=3
    )
@@ -574,7 +574,7 @@ print("TRIAGE: {} (conf={:.0%})".format(triage["response"], triage["confidence"]

 # Tier 2: escalate to Claude for deep analysis if Tier 1 is uncertain
 if triage["confidence"] < 0.88:
-    deep_llm = LiteLLM(model="anthropic/claude-sonnet-5")
+    deep_llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
    deep = context.query_with_reasoning(
        "Full MITRE ATT&CK analysis of this alert: identify the attack chain, "
        "blast radius, affected systems, and recommended containment steps.",
@@ -630,7 +630,7 @@ for d in drugs:
 # trastuzumab (conf=0.98), pertuzumab (conf=0.97), docetaxel (conf=0.96)

 # Report synthesis with Claude — switch to azure/gpt-4o for HIPAA by changing one string
-report_llm = LiteLLM(model="anthropic/claude-sonnet-5")
+report_llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
 # For HIPAA-constrained Azure deployment:
 # report_llm = LiteLLM(model="azure/gpt-4o", api_key="YOUR_AZURE_KEY")

@@ -682,7 +682,7 @@ question = (

 # Two-provider consensus — same query, same graph, different LLMs
 gpt4o  = OpenAI(model="gpt-4o", api_key="YOUR_OAI_KEY")
-claude = LiteLLM(model="anthropic/claude-sonnet-5")
+claude = LiteLLM(model="anthropic/claude-sonnet-4-20250514")

 answer_a = context.query_with_reasoning(question, llm_provider=gpt4o,  max_results=10)
 answer_b = context.query_with_reasoning(question, llm_provider=claude, max_results=10)
@@ -197,7 +197,7 @@ reasoning_agent.load("./pipeline/enriched_intel/")
 # All memories, graph nodes, and vector embeddings from both ingestion agents are now available.

 # Use a high-capability model for the synthesis step
-llm = LiteLLM(model="anthropic/claude-sonnet-5")
+llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")

 synthesis = reasoning_agent.query_with_reasoning(
    "Summarize the APT29 exploitation of CVE-2024-3400: affected products, "
@@ -428,7 +428,7 @@ tier1.store(

 # --- Tier 2: deep investigation when Tier 1 confidence is low ---
 if triage["confidence"] < 0.90:
-    deep_llm = LiteLLM(model="anthropic/claude-sonnet-5")
+    deep_llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")

    investigation = tier2.query_with_reasoning(
        "Full MITRE ATT&CK analysis of incident {}. "
@@ -533,7 +533,7 @@ t1.start(); t2.start()
 t1.join();  t2.join()

 # Chief agent synthesizes across literature and experimental data
-llm = LiteLLM(model="anthropic/claude-sonnet-5")
+llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")

 synthesis = chief.query_with_reasoning(
    "Identify the top two candidate compounds for KRAS G12C NSCLC that show "
@@ -576,7 +576,7 @@ credit_officer  = make_desk_agent()
 committee_chair = make_desk_agent()

 app_id = "LOAN-2025-88421"
-llm    = LiteLLM(model="anthropic/claude-sonnet-5")
+llm    = LiteLLM(model="anthropic/claude-sonnet-4-20250514")

 # --- Risk Desk: PD/LGD/EL analysis ---
 risk_desk.store(
@@ -477,7 +477,7 @@ regs = [
 ]

 # Use an LLM to extract the conceptual model from regulatory prose
-llm_gen  = LLMOntologyGenerator(provider="anthropic", model="claude-sonnet-5")
+llm_gen  = LLMOntologyGenerator(provider="anthropic", model="claude-sonnet-4-20250514")
 ontology = llm_gen.generate_ontology_from_text(
    "\n\n".join(r.text[:8000] for r in regs)  # token-safe excerpt per document
 )
@@ -100,15 +100,14 @@ ner = NamedEntityRecognizer(
    methods=["llm", "ml", "pattern"],
    confidence_threshold=0.75,
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
 )
 entities = ner.extract_entities(report)

 for e in entities:
    print("[{:>5.2f}]  {:15s}  {}".format(e.confidence, e.label, e.text))

-# Illustrative output — exact labels and scores depend on the method and model.
-# Abbreviated:
+# Expected output (abbreviated):
 # [ 0.94]  THREAT_ACTOR    GAMMA-7
 # [ 0.91]  THREAT_ACTOR    DELTA-3
 # [ 0.97]  MALWARE         HAMMERTOSS
@@ -263,18 +262,16 @@ from semantica.semantic_extract import TripletExtractor
 tri = TripletExtractor(
    method="llm",
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
    include_temporal=True,       # attach time context to triplets when available
    include_provenance=True,     # embed source document reference in each triplet
-    validate=False,              # return raw triplets; validate explicitly below
 )

 # Feed in the entities and relations you already extracted — the extractor
-# uses them to constrain what it produces
+# uses them to constrain and validate what it produces
 triplets = tri.extract_triplets(report, entities, relations)

 # Filter malformed triplets before serialisation
-# (extract_triplets validates automatically unless validate=False, as above)
 valid = tri.validate_triplets(triplets)
 print("Valid: {}/{}".format(len(valid), len(triplets)))

@@ -323,7 +320,7 @@ def ingest_intel_report(
        methods=[method, "pattern"],
        confidence_threshold=0.70,
        provider="anthropic",
-        llm_model="claude-sonnet-5",
+        llm_model="claude-sonnet-4-6",
    )
    entities = ner.extract_entities(text)
    classified = ner.classify_entities(entities)
@@ -338,7 +335,7 @@ def ingest_intel_report(
        relation_types=["deployed", "targets", "exploits", "operates_from", "provided_to"],
        confidence_threshold=0.65,
        provider="anthropic",
-        llm_model="claude-sonnet-5",
+        llm_model="claude-sonnet-4-6",
    )
    relations = rel.extract_relations(text, entities)

@@ -350,10 +347,9 @@ def ingest_intel_report(
    tri = TripletExtractor(
        method=method,
        provider="anthropic",
-        llm_model="claude-sonnet-5",
+        llm_model="claude-sonnet-4-6",
        include_temporal=True,
        include_provenance=True,
-        validate=False,          # keep raw triplets so the summary can report rejections
    )
    triplets = tri.extract_triplets(text, entities, relations)
    valid    = tri.validate_triplets(triplets)
@@ -381,7 +377,6 @@ def ingest_intel_report(
        "coref_chains":   len(chains),
        "relations":      len(relations),
        "events":         len(events),
-        "triplets_total": len(triplets),
        "triplets_valid": len(valid),
        "graph_nodes":    graph_stats.get("graph_nodes", 0),
        "graph_edges":    graph_stats.get("graph_edges", 0),
@@ -407,7 +402,7 @@ for text, doc_id in reports:
        summary["relations"],
        summary["events"],
        summary["triplets_valid"],
-        summary["triplets_total"],
+        len(summary["rdf_turtle"]),
    ))
 ```

@@ -426,7 +421,7 @@ ner = NamedEntityRecognizer(
    methods=["llm", "pattern"],
    confidence_threshold=0.75,
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
 )
 entities = ner.extract_entities(fintel_text)
 grouped  = ner.classify_entities(entities)
@@ -443,14 +438,14 @@ rel = RelationExtractor(
    relation_types=["operates_from", "deployed", "targets", "exploits"],
    confidence_threshold=0.70,
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
 )
 relations = rel.extract_relations(fintel_text, entities)

 tri = TripletExtractor(
    method="llm",
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
    include_temporal=True,
    include_provenance=True,
 )
@@ -549,14 +544,14 @@ rel = RelationExtractor(
    relation_types=["treats", "causes_adverse_event", "has_efficacy", "evaluated_in"],
    confidence_threshold=0.65,
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
 )
 relations = rel.extract_relations(paper, entities)

 tri = TripletExtractor(
    method="llm",
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
    triplet_types=["treats", "has_efficacy", "causes_adverse_event"],
    include_temporal=True,
    include_provenance=True,
@@ -600,7 +595,7 @@ ner = NamedEntityRecognizer(
    methods=["llm", "ml", "pattern"],
    confidence_threshold=0.70,
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
 )
 entities = ner.extract_entities(credit_memo)
 grouped  = ner.classify_entities(entities)
@@ -617,14 +612,14 @@ rel = RelationExtractor(
    relation_types=["guaranteed_by", "secured_by", "classified_as", "exposed_to"],
    confidence_threshold=0.65,
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
 )
 relations = rel.extract_relations(credit_memo, entities)

 tri = TripletExtractor(
    method="llm",
    provider="anthropic",
-    llm_model="claude-sonnet-5",
+    llm_model="claude-sonnet-4-6",
    include_temporal=True,
    include_provenance=True,
 )
@@ -129,7 +129,7 @@ from semantica.llms import Groq, OpenAI, LiteLLM, HuggingFaceLLM
    from semantica.llms import LiteLLM

    llm = LiteLLM(
-        model="anthropic/claude-sonnet-5",
+        model="anthropic/claude-sonnet-4-20250514",
        api_key=os.getenv("ANTHROPIC_API_KEY"),
        temperature=0.0,
    )
@@ -198,7 +198,7 @@ llm = Groq(api_key=os.getenv("GROQ_API_KEY"), model="llama-3.1-8b-instant")
 # Method 3: Multiple providers via LiteLLM
 providers = {
    "fast": LiteLLM(model="groq/llama-3.1-8b-instant", api_key=os.getenv("GROQ_API_KEY")),
-    "smart": LiteLLM(model="anthropic/claude-sonnet-5", api_key=os.getenv("ANTHROPIC_API_KEY"))
+    "smart": LiteLLM(model="anthropic/claude-sonnet-4-20250514", api_key=os.getenv("ANTHROPIC_API_KEY"))
 }
 ```

@@ -252,7 +252,7 @@ from semantica.llms import LiteLLM
 # pip install "semantica[llm-litellm]"

 # Anthropic Claude
-llm = LiteLLM(model="anthropic/claude-opus-4-7",         api_key=os.getenv("ANTHROPIC_API_KEY"))
+llm = LiteLLM(model="anthropic/claude-opus-4-5",         api_key=os.getenv("ANTHROPIC_API_KEY"))

 # Google Gemini
 llm = LiteLLM(model="gemini/gemini-1.5-pro",             api_key=os.getenv("GOOGLE_API_KEY"))
@@ -267,7 +267,7 @@ llm = LiteLLM(model="deepseek/deepseek-chat",            api_key=os.getenv("DEEP
 llm = LiteLLM(model="azure/gpt-4o",                      api_key=os.getenv("AZURE_API_KEY"))

 # AWS Bedrock
-llm = LiteLLM(model="bedrock/anthropic.claude-sonnet-4-5-20250929-v1:0")
+llm = LiteLLM(model="bedrock/anthropic.claude-3-5-sonnet-20241022-v2:0")

 # Novita AI
 llm = LiteLLM(model="novita/deepseek/deepseek-v3.2",     api_key=os.getenv("NOVITA_API_KEY"))
@@ -297,12 +297,12 @@ from semantica.llms import LiteLLM

 # Pattern: LiteLLM(model="<provider>/<model-name>")
 providers = {
-    "Anthropic":  LiteLLM(model="anthropic/claude-opus-4-7",       api_key=os.getenv("ANTHROPIC_API_KEY")),
+    "Anthropic":  LiteLLM(model="anthropic/claude-opus-4-5",       api_key=os.getenv("ANTHROPIC_API_KEY")),
    "Gemini":     LiteLLM(model="gemini/gemini-1.5-pro",            api_key=os.getenv("GOOGLE_API_KEY")),
    "Ollama":     LiteLLM(model="ollama/llama3.2:3b",               api_base="http://localhost:11434"),
    "DeepSeek":   LiteLLM(model="deepseek/deepseek-chat",           api_key=os.getenv("DEEPSEEK_API_KEY")),
    "Azure":      LiteLLM(model="azure/gpt-4o",                     api_key=os.getenv("AZURE_API_KEY")),
-    "Bedrock":    LiteLLM(model="bedrock/anthropic.claude-sonnet-4-5-20250929-v1:0"),
+    "Bedrock":    LiteLLM(model="bedrock/anthropic.claude-3-5-sonnet-20241022-v2:0"),
    "Cohere":     LiteLLM(model="cohere/command-r-plus",            api_key=os.getenv("COHERE_API_KEY")),
    "Novita AI":  LiteLLM(model="novita/deepseek/deepseek-v3.2",    api_key=os.getenv("NOVITA_API_KEY")),
 }
@@ -416,7 +416,7 @@ for text in texts:
 | :---------- | :--------------------------- | :----------- |
 | **Entity Extraction** | `Groq("llama-3.3-70b-versatile")` | Fast, good accuracy for structured tasks |
 | **Relation Extraction** | `OpenAI("gpt-4o")` | Best at complex relationship reasoning |
-| **Complex Analysis** | `LiteLLM("anthropic/claude-sonnet-5")` | Highest reasoning capability |
+| **Complex Analysis** | `LiteLLM("anthropic/claude-sonnet-4-20250514")` | Highest reasoning capability |
 | **High Volume/Cost** | `LiteLLM("deepseek/deepseek-chat")` | Lowest cost per token |

 ### Error Handling
@@ -22,7 +22,6 @@ icon: "sitemap"
 | `LLMOntologyGenerator` | LLM-powered ontology generation for complex domains |
 | `SHACLGenerator` | Generate SHACL shapes from an ontology or KG schema |
 | `OntologyValidator` | Validate any graph against SHACL shapes: returns `SHACLValidationReport` |
-| `OntologyQualityGate` | Run deterministic ontology/KG quality checks for CI |
 | `OWLGenerator` | Serialize ontologies to Turtle, RDF/XML, JSON-LD |
 | `NamespaceManager` | IRI generation, prefix management, and namespace binding |
 | `OntologyEvaluator` | Coverage, completeness, and granularity quality metrics |
@@ -82,38 +81,9 @@ engine.export_owl(ontology, "ontology.ttl", format="turtle")
 | :------ | :----------- |
 | `from_data(data)` | Run the 5-stage pipeline on entity/relationship data |
 | `validate_graph(kg, ontology=...)` | Check a knowledge graph against generated SHACL shapes |
-| `quality_check(ontology, graph_data=...)` | Return a deterministic quality report and CI-friendly pass/fail result |
 | `export_owl(ontology, path, format)` | Serialize to `"turtle"`, `"xml"`, or `"json-ld"` |
 | `evaluate(ontology, kg)` | Compute coverage, completeness, and granularity metrics |

-### Ontology Quality Gate
-
-Use the quality gate before export or deployment to catch structural issues
-without adding a runtime dependency:
-
-```python
-from semantica.ontology import ontology_quality_check
-
-report = ontology_quality_check(
-    ontology,
-    graph_data=kg,
-    thresholds={"min_coverage": 0.8},
-)
-
-if not report.passed:
-    for issue in report.issues:
-        print(issue.code, issue.message)
-```
-
-The report checks class/property coverage, orphan schema elements, domain and
-range references, and unresolved KG relationship endpoints. It includes
-machine-readable issue codes, severity, counts, metrics, and threshold
-failures. The first version reports findings only; it does not auto-fix data.
-
-### Thresholds
-
-`min_coverage` (default `0.0`) sets the minimum required `coverage` score, the average of class and property coverage from `0.0` to `1.0`; the gate fails below it. `max_errors` (default `0.0`) caps how many `error`/`critical` issues are allowed before the gate fails. `max_warnings` (default `None`) caps `warning` issues the same way, and `None` means warnings alone never fail the gate. `fail_on_warnings` is a separate parameter, not a `thresholds` key, passed to `OntologyQualityGate(...)` or `.check(...)` directly; when `True`, a single warning fails the gate regardless of `max_warnings`.
-
 ## OntologyGenerator (5-Stage Pipeline)

 **`OntologyGenerator`** auto-generates a formal ontology from your knowledge graph entities and relationships:
@@ -33,9 +33,7 @@
      "devDependencies": {
        "@babel/core": "^7.29.6",
        "@eslint/js": "^9.39.4",
-        "@testing-library/react": "^16.3.3",
        "@types/babel__core": "^7.20.5",
-        "@types/jsdom": "^21.1.7",
        "@types/node": "^24.12.0",
        "@types/react": "^19.2.14",
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      "integrity": "sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ==",
      "license": "MIT"
    },
-    "node_modules/jsdom": {
-      "version": "26.1.0",
-      "resolved": "https://registry.npmmirror.com/jsdom/-/jsdom-26.1.0.tgz",
-      "integrity": "sha512-Cvc9WUhxSMEo4McES3P7oK3QaXldCfNWp7pl2NNeiIFlCoLr3kfq9kb1fxftiwk1FLV7CvpvDfonxtzUDeSOPg==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "cssstyle": "^4.2.1",
-        "data-urls": "^5.0.0",
-        "decimal.js": "^10.5.0",
-        "html-encoding-sniffer": "^4.0.0",
-        "http-proxy-agent": "^7.0.2",
-        "https-proxy-agent": "^7.0.6",
-        "is-potential-custom-element-name": "^1.0.1",
-        "nwsapi": "^2.2.16",
-        "parse5": "^7.2.1",
-        "rrweb-cssom": "^0.8.0",
-        "saxes": "^6.0.0",
-        "symbol-tree": "^3.2.4",
-        "tough-cookie": "^5.1.1",
-        "w3c-xmlserializer": "^5.0.0",
-        "webidl-conversions": "^7.0.0",
-        "whatwg-encoding": "^3.1.1",
-        "whatwg-mimetype": "^4.0.0",
-        "whatwg-url": "^14.1.1",
-        "ws": "^8.18.0",
-        "xml-name-validator": "^5.0.0"
-      },
-      "engines": {
-        "node": ">=18"
-      },
-      "peerDependencies": {
-        "canvas": "^3.0.0"
-      },
-      "peerDependenciesMeta": {
-        "canvas": {
-          "optional": true
-        }
-      }
-    },
    "node_modules/jsesc": {
      "version": "3.1.0",
      "resolved": "https://registry.npmjs.org/jsesc/-/jsesc-3.1.0.tgz",
@@ -3739,17 +3321,6 @@
        "react": "^16.5.1 || ^17.0.0 || ^18.0.0 || ^19.0.0"
      }
    },
-    "node_modules/lz-string": {
-      "version": "1.5.0",
-      "resolved": "https://registry.npmmirror.com/lz-string/-/lz-string-1.5.0.tgz",
-      "integrity": "sha512-h5bgJWpxJNswbU7qCrV0tIKQCaS3blPDrqKWx+QxzuzL1zGUzij9XCWLrSLsJPu5t+eWA/ycetzYAO5IOMcWAQ==",
-      "dev": true,
-      "license": "MIT",
-      "peer": true,
-      "bin": {
-        "lz-string": "bin/bin.js"
-      }
-    },
    "node_modules/markdown-table": {
      "version": "3.0.4",
      "resolved": "https://registry.npmjs.org/markdown-table/-/markdown-table-3.0.4.tgz",
@@ -4712,13 +4283,6 @@
        "node": ">=18"
      }
    },
-    "node_modules/nwsapi": {
-      "version": "2.2.27",
-      "resolved": "https://registry.npmmirror.com/nwsapi/-/nwsapi-2.2.27.tgz",
-      "integrity": "sha512-gQPNF78qebCQ6tvVFBYrvJdBNOrYZm90ZlXgpIFm06p6qHDHq/XC4TnJftN6OMbxVE0UTBAoRgcsDeJBBooITw==",
-      "dev": true,
-      "license": "MIT"
-    },
    "node_modules/object-assign": {
      "version": "4.1.1",
      "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz",
@@ -4818,19 +4382,6 @@
      "integrity": "sha512-CmBKiL6NNo/OqgmMn95Fk9Whlp2mtvIv+KNpQKN2F4SjvrEesubTRWGYSg+BnWZOnlCaSTU1sMpsBOzgbYhnsA==",
      "license": "MIT"
    },
-    "node_modules/parse5": {
-      "version": "7.3.0",
-      "resolved": "https://registry.npmmirror.com/parse5/-/parse5-7.3.0.tgz",
-      "integrity": "sha512-IInvU7fabl34qmi9gY8XOVxhYyMyuH2xUNpb2q8/Y+7552KlejkRvqvD19nMoUW/uQGGbqNpA6Tufu5FL5BZgw==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "entities": "^6.0.0"
-      },
-      "funding": {
-        "url": "https://github.com/inikulin/parse5?sponsor=1"
-      }
-    },
    "node_modules/path-exists": {
      "version": "4.0.0",
      "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
@@ -4954,30 +4505,6 @@
        "node": ">= 0.8.0"
      }
    },
-    "node_modules/pretty-format": {
-      "version": "27.5.1",
-      "resolved": "https://registry.npmmirror.com/pretty-format/-/pretty-format-27.5.1.tgz",
-      "integrity": "sha512-Qb1gy5OrP5+zDf2Bvnzdl3jsTf1qXVMazbvCoKhtKqVs4/YK4ozX4gKQJJVyNe+cajNPn0KoC0MC3FUmaHWEmQ==",
-      "dev": true,
-      "license": "MIT",
-      "peer": true,
-      "dependencies": {
-        "ansi-regex": "^5.0.1",
-        "ansi-styles": "^5.0.0",
-        "react-is": "^17.0.1"
-      },
-      "engines": {
-        "node": "^10.13.0 || ^12.13.0 || ^14.15.0 || >=15.0.0"
-      }
-    },
-    "node_modules/pretty-format/node_modules/react-is": {
-      "version": "17.0.2",
-      "resolved": "https://registry.npmmirror.com/react-is/-/react-is-17.0.2.tgz",
-      "integrity": "sha512-w2GsyukL62IJnlaff/nRegPQR94C/XXamvMWmSHRJ4y7Ts/4ocGRmTHvOs8PSE6pB3dWOrD/nueuU5sduBsQ4w==",
-      "dev": true,
-      "license": "MIT",
-      "peer": true
-    },
    "node_modules/prop-types": {
      "version": "15.8.1",
      "resolved": "https://registry.npmjs.org/prop-types/-/prop-types-15.8.1.tgz",
@@ -5290,33 +4817,6 @@
        "fsevents": "~2.3.2"
      }
    },
-    "node_modules/rrweb-cssom": {
-      "version": "0.8.0",
-      "resolved": "https://registry.npmmirror.com/rrweb-cssom/-/rrweb-cssom-0.8.0.tgz",
-      "integrity": "sha512-guoltQEx+9aMf2gDZ0s62EcV8lsXR+0w8915TC3ITdn2YueuNjdAYh/levpU9nFaoChh9RUS5ZdQMrKfVEN9tw==",
-      "dev": true,
-      "license": "MIT"
-    },
-    "node_modules/safer-buffer": {
-      "version": "2.1.2",
-      "resolved": "https://registry.npmmirror.com/safer-buffer/-/safer-buffer-2.1.2.tgz",
-      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==",
-      "dev": true,
-      "license": "MIT"
-    },
-    "node_modules/saxes": {
-      "version": "6.0.0",
-      "resolved": "https://registry.npmmirror.com/saxes/-/saxes-6.0.0.tgz",
-      "integrity": "sha512-xAg7SOnEhrm5zI3puOOKyy1OMcMlIJZYNJY7xLBwSze0UjhPLnWfj2GF2EpT0jmzaJKIWKHLsaSSajf35bcYnA==",
-      "dev": true,
-      "license": "ISC",
-      "dependencies": {
-        "xmlchars": "^2.2.0"
-      },
-      "engines": {
-        "node": ">=v12.22.7"
-      }
-    },
    "node_modules/scheduler": {
      "version": "0.27.0",
      "resolved": "https://registry.npmjs.org/scheduler/-/scheduler-0.27.0.tgz",
@@ -5424,13 +4924,6 @@
        "inline-style-parser": "0.2.7"
      }
    },
-    "node_modules/symbol-tree": {
-      "version": "3.2.4",
-      "resolved": "https://registry.npmmirror.com/symbol-tree/-/symbol-tree-3.2.4.tgz",
-      "integrity": "sha512-9QNk5KwDF+Bvz+PyObkmSYjI5ksVUYtjW7AU22r2NKcfLJcXp96hkDWU3+XndOsUb+AQ9QhfzfCT2O+CNWT5Tw==",
-      "dev": true,
-      "license": "MIT"
-    },
    "node_modules/tinyglobby": {
      "version": "0.2.16",
      "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.16.tgz",
@@ -5448,52 +4941,6 @@
        "url": "https://github.com/sponsors/SuperchupuDev"
      }
    },
-    "node_modules/tldts": {
-      "version": "6.1.86",
-      "resolved": "https://registry.npmmirror.com/tldts/-/tldts-6.1.86.tgz",
-      "integrity": "sha512-WMi/OQ2axVTf/ykqCQgXiIct+mSQDFdH2fkwhPwgEwvJ1kSzZRiinb0zF2Xb8u4+OqPChmyI6MEu4EezNJz+FQ==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "tldts-core": "^6.1.86"
-      },
-      "bin": {
-        "tldts": "bin/cli.js"
-      }
-    },
-    "node_modules/tldts-core": {
-      "version": "6.1.86",
-      "resolved": "https://registry.npmmirror.com/tldts-core/-/tldts-core-6.1.86.tgz",
-      "integrity": "sha512-Je6p7pkk+KMzMv2XXKmAE3McmolOQFdxkKw0R8EYNr7sELW46JqnNeTX8ybPiQgvg1ymCoF8LXs5fzFaZvJPTA==",
-      "dev": true,
-      "license": "MIT"
-    },
-    "node_modules/tough-cookie": {
-      "version": "5.1.2",
-      "resolved": "https://registry.npmmirror.com/tough-cookie/-/tough-cookie-5.1.2.tgz",
-      "integrity": "sha512-FVDYdxtnj0G6Qm/DhNPSb8Ju59ULcup3tuJxkFb5K8Bv2pUXILbf0xZWU8PX8Ov19OXljbUyveOFwRMwkXzO+A==",
-      "dev": true,
-      "license": "BSD-3-Clause",
-      "dependencies": {
-        "tldts": "^6.1.32"
-      },
-      "engines": {
-        "node": ">=16"
-      }
-    },
-    "node_modules/tr46": {
-      "version": "5.1.1",
-      "resolved": "https://registry.npmmirror.com/tr46/-/tr46-5.1.1.tgz",
-      "integrity": "sha512-hdF5ZgjTqgAntKkklYw0R03MG2x/bSzTtkxmIRw/sTNV8YXsCJ1tfLAX23lhxhHJlEf3CRCOCGGWw3vI3GaSPw==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "punycode": "^2.3.1"
-      },
-      "engines": {
-        "node": ">=18"
-      }
-    },
    "node_modules/trim-lines": {
      "version": "3.0.1",
      "resolved": "https://registry.npmjs.org/trim-lines/-/trim-lines-3.0.1.tgz",
@@ -5917,67 +5364,6 @@
        }
      }
    },
-    "node_modules/w3c-xmlserializer": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmmirror.com/w3c-xmlserializer/-/w3c-xmlserializer-5.0.0.tgz",
-      "integrity": "sha512-o8qghlI8NZHU1lLPrpi2+Uq7abh4GGPpYANlalzWxyWteJOCsr/P+oPBA49TOLu5FTZO4d3F9MnWJfiMo4BkmA==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "xml-name-validator": "^5.0.0"
-      },
-      "engines": {
-        "node": ">=18"
-      }
-    },
-    "node_modules/webidl-conversions": {
-      "version": "7.0.0",
-      "resolved": "https://registry.npmmirror.com/webidl-conversions/-/webidl-conversions-7.0.0.tgz",
-      "integrity": "sha512-VwddBukDzu71offAQR975unBIGqfKZpM+8ZX6ySk8nYhVoo5CYaZyzt3YBvYtRtO+aoGlqxPg/B87NGVZ/fu6g==",
-      "dev": true,
-      "license": "BSD-2-Clause",
-      "engines": {
-        "node": ">=12"
-      }
-    },
-    "node_modules/whatwg-encoding": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmmirror.com/whatwg-encoding/-/whatwg-encoding-3.1.1.tgz",
-      "integrity": "sha512-6qN4hJdMwfYBtE3YBTTHhoeuUrDBPZmbQaxWAqSALV/MeEnR5z1xd8UKud2RAkFoPkmB+hli1TZSnyi84xz1vQ==",
-      "deprecated": "Use @exodus/bytes instead for a more spec-conformant and faster implementation",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "iconv-lite": "0.6.3"
-      },
-      "engines": {
-        "node": ">=18"
-      }
-    },
-    "node_modules/whatwg-mimetype": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmmirror.com/whatwg-mimetype/-/whatwg-mimetype-4.0.0.tgz",
-      "integrity": "sha512-QaKxh0eNIi2mE9p2vEdzfagOKHCcj1pJ56EEHGQOVxp8r9/iszLUUV7v89x9O1p/T+NlTM5W7jW6+cz4Fq1YVg==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=18"
-      }
-    },
-    "node_modules/whatwg-url": {
-      "version": "14.2.0",
-      "resolved": "https://registry.npmmirror.com/whatwg-url/-/whatwg-url-14.2.0.tgz",
-      "integrity": "sha512-De72GdQZzNTUBBChsXueQUnPKDkg/5A5zp7pFDuQAj5UFoENpiACU0wlCvzpAGnTkj++ihpKwKyYewn/XNUbKw==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "tr46": "^5.1.0",
-        "webidl-conversions": "^7.0.0"
-      },
-      "engines": {
-        "node": ">=18"
-      }
-    },
    "node_modules/which": {
      "version": "2.0.2",
      "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
@@ -6004,45 +5390,6 @@
        "node": ">=0.10.0"
      }
    },
-    "node_modules/ws": {
-      "version": "8.21.3",
-      "resolved": "https://registry.npmmirror.com/ws/-/ws-8.21.3.tgz",
-      "integrity": "sha512-201TZ/kPWxoPr/OKWjquZR1SWKXcvxdH+e1xrx89b3YbmzLMFCLfnaG1HFIgWzJOEWZ7MvpK++odZufgYR50Rw==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=10.0.0"
-      },
-      "peerDependencies": {
-        "bufferutil": "^4.0.1",
-        "utf-8-validate": ">=5.0.2"
-      },
-      "peerDependenciesMeta": {
-        "bufferutil": {
-          "optional": true
-        },
-        "utf-8-validate": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/xml-name-validator": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmmirror.com/xml-name-validator/-/xml-name-validator-5.0.0.tgz",
-      "integrity": "sha512-EvGK8EJ3DhaHfbRlETOWAS5pO9MZITeauHKJyb8wyajUfQUenkIg2MvLDTZ4T/TgIcm3HU0TFBgWWboAZ30UHg==",
-      "dev": true,
-      "license": "Apache-2.0",
-      "engines": {
-        "node": ">=18"
-      }
-    },
-    "node_modules/xmlchars": {
-      "version": "2.2.0",
-      "resolved": "https://registry.npmmirror.com/xmlchars/-/xmlchars-2.2.0.tgz",
-      "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==",
-      "dev": true,
-      "license": "MIT"
-    },
    "node_modules/xss": {
      "version": "1.0.15",
      "resolved": "https://registry.npmjs.org/xss/-/xss-1.0.15.tgz",
@@ -9,7 +9,6 @@
    "lint": "eslint .",
    "preview": "vite preview",
    "test:graph-store": "node --test tests/graphStore.multi-edge.test.mjs",
-    "test:graph-workspace": "node --import tsx --test tests/markdownContentViewer.test.ts tests/markdownEditorInteraction.test.tsx tests/markdownEditorState.test.ts tests/nodeMarkdownSync.test.ts tests/graphSceneState.display.test.ts tests/temporalLifecycle.test.ts tests/deterministicExplorerRendering.test.ts tests/explorerCapabilities.test.tsx tests/smallGraphLayout.test.ts tests/realtimeGraphAttributes.test.ts",
    "test:graph-workspace": "node --import tsx --test tests/markdownContentViewer.test.ts tests/graphSceneState.display.test.ts tests/temporalLifecycle.test.ts tests/deterministicExplorerRendering.test.ts tests/smallGraphLayout.test.ts tests/realtimeGraphAttributes.test.ts tests/ontologyEditorModel.test.ts",
    "test:deterministic-e2e": "node --import tsx --test tests/deterministicExplorerRendering.e2e.ts",
    "test:plugin-registry": "node --import tsx --test tests/pluginRegistry.temporal.test.mjs"
@@ -40,9 +39,7 @@
  "devDependencies": {
    "@babel/core": "^7.29.6",
    "@eslint/js": "^9.39.4",
-    "@testing-library/react": "^16.3.3",
    "@types/babel__core": "^7.20.5",
-    "@types/jsdom": "^21.1.7",
    "@types/node": "^24.12.0",
    "@types/react": "^19.2.14",
    "@types/react-dom": "^19.2.3",
@@ -52,7 +49,6 @@
    "eslint-plugin-react-hooks": "^7.0.1",
    "eslint-plugin-react-refresh": "^0.5.2",
    "globals": "^17.4.0",
-    "jsdom": "^26.1.0",
    "tsx": "^4.21.0",
    "typescript": "~5.9.3",
    "typescript-eslint": "^8.57.0",
@@ -17,13 +17,10 @@ import {
  type LucideIcon,
 } from 'lucide-react';
 import { ErrorBoundary } from './ErrorBoundary';
-import { ExploreWorkspaceTabs, type ExploreView } from './ExploreWorkspaceTabs';
-import { fetchAgentMemoryAvailability } from './explorerCapabilities';

 const DecisionWorkspace = lazy(() => import('./workspaces/DecisionWorkspace/DecisionWorkspace').then((module) => ({ default: module.DecisionWorkspace })));
 const DiffMergeWorkspace = lazy(() => import('./workspaces/DiffMergeWorkspace/DiffMergeWorkspace').then((module) => ({ default: module.DiffMergeWorkspace })));
 const GraphWorkspace = lazy(() => import('./workspaces/GraphWorkspace/GraphWorkspace').then((module) => ({ default: module.GraphWorkspace })));
-const MemoryWorkspace = lazy(() => import('./workspaces/MemoryWorkspace').then((module) => ({ default: module.MemoryWorkspace })));
 const ImportExportWorkspace = lazy(() => import('./workspaces/ImportExportWorkspace/ImportExportWorkspace').then((module) => ({ default: module.ImportExportWorkspace })));
 const LineageDiagram = lazy(() => import('./workspaces/LineageWorkspace/LineageDiagram').then((module) => ({ default: module.LineageDiagram })));
 const ReasoningWorkspace = lazy(() => import('./workspaces/ReasoningWorkspace').then((module) => ({ default: module.ReasoningWorkspace })));
@@ -36,6 +33,7 @@ const OntologySummaryTab = lazy(() => import('./workspaces/ManageWorkspace/Ontol
 const OntologyWorkspace = lazy(() => import('./workspaces/OntologyWorkspace').then((module) => ({ default: module.OntologyWorkspace })));

 type WorkspaceId = 'welcome' | 'explore' | 'analyze' | 'decisions' | 'enrich' | 'manage' | 'ontology-hub';
+type ExploreView = 'graph' | 'vocabulary';
 type AnalyzeView = 'sparql' | 'reasoning';
 type EnrichView = 'import' | 'merge' | 'registry' | 'resolve';
 type ManageView = 'lineage' | 'kg-overview' | 'ontology';
@@ -1793,37 +1791,6 @@ export default function App() {
  const [enrichView, setEnrichView] = useState<EnrichView>('import');
  const [manageView, setManageView] = useState<ManageView>('lineage');
  const [graphFocusRequest, setGraphFocusRequest] = useState<{ nodeId: string; token: number } | null>(null);
-  const [exploreDraftDirty, setExploreDraftDirty] = useState(false);
-  const [agentMemoryAvailable, setAgentMemoryAvailable] = useState(false);
-
-  useEffect(() => {
-    let active = true;
-    void fetchAgentMemoryAvailability().then((available) => {
-      if (active) setAgentMemoryAvailable(available);
-    });
-    return () => {
-      active = false;
-    };
-  }, []);
-
-  const confirmDiscardExploreDraft = () => (
-    !exploreDraftDirty
-    || window.confirm("Discard the unapplied Markdown draft and leave this resource?")
-  );
-
-  const switchExploreView = (nextView: ExploreView) => {
-    if (nextView === exploreView) return;
-    if (!confirmDiscardExploreDraft()) return;
-    setExploreDraftDirty(false);
-    setExploreView(nextView);
-  };
-
-  const switchWorkspace = (nextWorkspace: WorkspaceId) => {
-    if (nextWorkspace === activeWorkspace) return;
-    if (activeWorkspace === "explore" && !confirmDiscardExploreDraft()) return;
-    setExploreDraftDirty(false);
-    setActiveWorkspace(nextWorkspace);
-  };


  const renderWorkspace = () => {
@@ -1856,15 +1823,18 @@ export default function App() {
      return (
        <WorkspaceShell
          title="Explore"
-          subtitle={exploreView === 'graph' ? undefined : exploreView === 'memories' ? "Browse and edit canonical AgentMemory documents." : "Browse the graph and switch views without leaving the workspace."}
-          kicker={exploreView === 'graph' ? 'Graph Studio' : exploreView === 'memories' ? 'Memory Browser' : 'Vocabulary Browser'}
+          subtitle={exploreView === 'graph' ? undefined : "Browse the graph and switch views without leaving the workspace."}
+          kicker={exploreView === 'graph' ? 'Graph Studio' : 'Vocabulary Browser'}
          compact
          tabs={
-            <ExploreWorkspaceTabs
-              activeView={exploreView}
-              agentMemoryAvailable={agentMemoryAvailable}
-              onSelect={switchExploreView}
-            />
+            <>
+              <button className="workspace-tab" data-active={exploreView === 'graph'} onClick={() => setExploreView('graph')}>
+                Semantica Explorer
+              </button>
+              <button className="workspace-tab" data-active={exploreView === 'vocabulary'} onClick={() => setExploreView('vocabulary')}>
+                Vocabulary Browser
+              </button>
+            </>
          }
        >
          <ErrorBoundary key={`explore-${exploreView}`}>
@@ -1873,9 +1843,8 @@ export default function App() {
                <GraphWorkspace
                  externalFocusNodeId={graphFocusRequest?.nodeId}
                  externalFocusToken={graphFocusRequest?.token}
-                  onDirtyChange={setExploreDraftDirty}
                />
-              ) : exploreView === 'memories' ? <MemoryWorkspace onDirtyChange={setExploreDraftDirty} /> : <VocabularyWorkspace />}
+              ) : <VocabularyWorkspace />}
            </Suspense>
          </ErrorBoundary>
        </WorkspaceShell>
@@ -2020,13 +1989,13 @@ export default function App() {
      <style>{shellStyles}</style>
      <div className="app-shell">
        <aside className="app-rail">
-          <button className="brand-pill" title="Semantica Knowledge Explorer" onClick={() => switchWorkspace('welcome')} style={{ cursor: 'pointer', border: '1px solid rgba(127,208,255,0.18)' }}>SKE</button>
+          <button className="brand-pill" title="Semantica Knowledge Explorer" onClick={() => setActiveWorkspace('welcome')} style={{ cursor: 'pointer', border: '1px solid rgba(127,208,255,0.18)' }}>SKE</button>
          {navItems.map(({ id, label, hint, icon: Icon }) => (
            <button
              key={id}
              className="nav-button"
              data-active={activeWorkspace === id}
-              onClick={() => switchWorkspace(id)}
+              onClick={() => setActiveWorkspace(id)}
              title={hint}
            >
              <Icon size={20} />
@@ -1,29 +0,0 @@
-export type ExploreView = 'graph' | 'memories' | 'vocabulary';
-
-type ExploreWorkspaceTabsProps = {
-  activeView: ExploreView;
-  agentMemoryAvailable: boolean;
-  onSelect: (view: ExploreView) => void;
-};
-
-export function ExploreWorkspaceTabs({
-  activeView,
-  agentMemoryAvailable,
-  onSelect,
-}: ExploreWorkspaceTabsProps) {
-  return (
-    <>
-      <button className="workspace-tab" data-active={activeView === 'graph'} onClick={() => onSelect('graph')}>
-        Semantica Explorer
-      </button>
-      {agentMemoryAvailable ? (
-        <button className="workspace-tab" data-active={activeView === 'memories'} onClick={() => onSelect('memories')}>
-          Memories
-        </button>
-      ) : null}
-      <button className="workspace-tab" data-active={activeView === 'vocabulary'} onClick={() => onSelect('vocabulary')}>
-        Vocabulary Browser
-      </button>
-    </>
-  );
-}
@@ -1,24 +0,0 @@
-type Fetcher = (
-  input: RequestInfo | URL,
-  init?: RequestInit,
-) => Promise<Response>;
-
-type ExplorerInfo = {
-  capabilities?: {
-    agent_memory?: boolean;
-  };
-};
-
-export async function fetchAgentMemoryAvailability(
-  fetcher: Fetcher = fetch,
-): Promise<boolean> {
-  try {
-    const response = await fetcher('/api/info');
-    if (!response.ok) return false;
-
-    const info = await response.json() as ExplorerInfo;
-    return info.capabilities?.agent_memory === true;
-  } catch {
-    return false;
-  }
-}
@@ -15,7 +15,6 @@ export type RegistryEntryOp =
  | "export"
  | "merge"
  | "add-node"
-  | "update-node"
  | "add-edge"
  | "delete"
  | "infer"
@@ -16,7 +16,6 @@ const OP_META: Record<
  export:       { label: "EXPORT",       color: "#8fa8c6", bg: "rgba(143,168,198,0.08)", border: "rgba(143,168,198,0.18)" },
  merge:        { label: "MERGE",        color: "#f2b66d", bg: "rgba(242,182,109,0.12)", border: "rgba(242,182,109,0.28)" },
  "add-node":   { label: "ADD NODE",     color: "#4cc38a", bg: "rgba(76,195,138,0.12)",  border: "rgba(76,195,138,0.28)" },
-  "update-node": { label: "UPDATE NODE",  color: "#79c0ff", bg: "rgba(121,192,255,0.10)", border: "rgba(121,192,255,0.24)" },
  "add-edge":   { label: "ADD EDGE",     color: "#4cc38a", bg: "rgba(76,195,138,0.10)",  border: "rgba(76,195,138,0.22)" },
  delete:       { label: "DELETE",       color: "#ff7b72", bg: "rgba(255,123,114,0.12)", border: "rgba(255,123,114,0.28)" },
  infer:        { label: "INFER",        color: "#d2a8ff", bg: "rgba(210,168,255,0.12)", border: "rgba(210,168,255,0.28)" },
@@ -24,7 +23,7 @@ const OP_META: Record<
 };

 const ALL_OPS: (RegistryEntryOp | "all")[] = [
-  "all", "import", "export", "merge", "add-node", "update-node", "add-edge", "infer", "delete", "vocab-import",
+  "all", "import", "export", "merge", "add-node", "add-edge", "infer", "delete", "vocab-import",
 ];

 function formatTimestamp(date: Date): string {
@@ -4,7 +4,6 @@ import { graph } from "../../store/graphStore";
 import { GRAPH_THEME, withAlpha } from "./graphTheme";
 import type { GraphSelectedNodeKind } from "./types";
 import { MarkdownContentViewer } from "./MarkdownContentViewer";
-import type { MarkdownApplyResult } from "./markdownResourceClient";

 export type LinkPrediction = {
  target: string;
@@ -45,8 +44,6 @@ export interface GraphInspectorPanelProps {
  pathResult: PathResponse | null;
  onDownloadProvenance: (format: "json" | "markdown") => void;
  onFocusNode?: (nodeId: string) => void;
-  onMarkdownApplied?: (result: MarkdownApplyResult) => void;
-  onMarkdownDirtyChange?: (dirty: boolean) => void;
 }

 const PROVENANCE_KEYS = ["source", "source_url", "pmid", "pmids", "evidence", "provenance", "confidence"] as const;
@@ -307,8 +304,6 @@ export function GraphInspectorPanel({
  pathResult,
  onDownloadProvenance,
  onFocusNode,
-  onMarkdownApplied,
-  onMarkdownDirtyChange,
 }: GraphInspectorPanelProps) {
  if (!nodeId) {
    return (
@@ -419,18 +414,19 @@ export function GraphInspectorPanel({
        </div>
      ) : null}

-      {/* Canonical nodes remain editable even when their current body is empty. */}
-      <details className="node-panel-collapse" open>
-        <summary className="node-panel-summary">Content</summary>
-        <div className="node-panel-body" style={{ marginTop: 8 }}>
-          <MarkdownContentViewer
-            content={nodeContent}
-            resource={{ kind: "context-node", id: effectiveNodeId }}
-            onApplied={onMarkdownApplied}
-            onDirtyChange={onMarkdownDirtyChange}
-          />
-        </div>
-      </details>
+      {/* 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}>
@@ -44,12 +44,6 @@ import { createTemporalSnapshotGuards, type TemporalSnapshotResponse } from "./t
 import { SMALL_GRAPH_MAX_NODES } from "./smallGraphLayout";
 import { buildRealtimeEdgeAttributes } from "./realtimeGraphAttributes";
 import type { LinkPrediction, PathResponse } from "./GraphInspectorPanel";
-import type { MarkdownApplyResult } from "./markdownResourceClient";
-import {
-  NodeMarkdownRefreshGuard,
-  buildNodeMarkdownAttributeUpdate,
-  readNodeMarkdownAttributeUpdate,
-} from "./nodeMarkdownSync";
 import type { GraphSceneHandle, GraphSceneRuntime } from "./scene";
 import type {
  GraphAnalyticsSnapshot,
@@ -1247,10 +1241,9 @@ function collectPluginOverlays(
 interface GraphWorkspaceProps {
  externalFocusNodeId?: string;
  externalFocusToken?: number;
-  onDirtyChange?: (dirty: boolean) => void;
 }

-export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirtyChange }: GraphWorkspaceProps = {}) {
+export function GraphWorkspace({ externalFocusNodeId, externalFocusToken }: GraphWorkspaceProps = {}) {
  const [selectedNodeId, setSelectedNodeId] = useState("");
  const [focusedNodeId, setFocusedNodeId] = useState("");
  const [lastGroupedSelectedNodeId, setLastGroupedSelectedNodeId] = useState("");
@@ -1258,12 +1251,6 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
  const [isLayoutRunning, setIsLayoutRunning] = useState(false);
  const [graphReady, setGraphReady] = useState(false);
  const [graphVersion, setGraphVersion] = useState(0);
-  const [markdownDraftDirty, setMarkdownDraftDirty] = useState(false);
-  const markdownRefreshGuard = useMemo(() => new NodeMarkdownRefreshGuard(), []);
-  const handleMarkdownDirtyChange = useCallback((dirty: boolean) => {
-    setMarkdownDraftDirty(dirty);
-    onDirtyChange?.(dirty);
-  }, [onDirtyChange]);
  const [viewMode, setViewMode] = useState<GraphViewMode>("full");
  const [aggregationEnabled] = useState(true);
  const [collapsedNeighborhoodNodeIds, setCollapsedNeighborhoodNodeIds] = useState<string[]>([]);
@@ -1641,17 +1628,8 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
      : null,
    [viewMode, aggregationEnabled, collapsedNeighborhoodNodeIds, graphVersion],
  );
-  const confirmDiscardMarkdownDraft = useCallback(() => {
-    if (!markdownDraftDirty) return true;
-    const discard = window.confirm(
-      "Discard the unapplied Markdown draft and leave this node?",
-    );
-    return discard;
-  }, [markdownDraftDirty]);
-

  const requestViewMode = useCallback((nextViewMode: GraphViewMode) => {
-    if (nextViewMode !== viewMode && !confirmDiscardMarkdownDraft()) return;
    if (nextViewMode === "focused") {
      const resolution = resolveNodeIdForFocusedMode(selectedNodeId, pluginRuntimeRef.current?.displayGraph);
      if (!resolution.resolvedNodeId) {
@@ -1704,7 +1682,6 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
    ));
    setViewMode("full");
  }, [
-    confirmDiscardMarkdownDraft,
    aggregationEnabled,
    collapsedNeighborhoodNodeIds,
    focusedNodeId,
@@ -1715,11 +1692,9 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
    lastGroupedSelectedNodeId,
    resolveNodeIdForFocusedMode,
    selectedNodeId,
-    viewMode,
  ]);

  const focusNode = useCallback((nodeId: string) => {
-    if (nodeId !== selectedNodeId && !confirmDiscardMarkdownDraft()) return;
    if (!nodeId) {
      setSelectedNodeId("");
      setSelectedEdgeId("");
@@ -1745,18 +1720,14 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
      setFocusedNodeId(nextSelectedNodeId);
      setIsLayoutRunning(false);
    }
-  }, [confirmDiscardMarkdownDraft, selectedNodeId, viewMode]);  // Note: ego/heatmap/distanceMode effects re-run automatically when selectedNodeId changes
+  }, [viewMode]);  // Note: ego/heatmap/distanceMode effects re-run automatically when selectedNodeId changes

  useEffect(() => {
    if (!externalFocusNodeId || externalFocusToken == null) return;
    if (lastExternalFocusTokenRef.current === externalFocusToken) return;
    if (!graphReady || !graph.hasNode(externalFocusNodeId)) return;
-    if (
-      externalFocusNodeId !== selectedNodeId
-      && !confirmDiscardMarkdownDraft()
-    ) return;
-    lastExternalFocusTokenRef.current = externalFocusToken;

+    lastExternalFocusTokenRef.current = externalFocusToken;
    // Set state directly instead of going through focusNode(), which captures
    // a stale viewMode in its closure. setViewMode is called first so the node
    // is visible in the full graph before the scene pans to it.
@@ -1766,13 +1737,7 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
    window.setTimeout(() => {
      sceneRef.current?.focusNode(externalFocusNodeId);
    }, 0);
-  }, [
-    confirmDiscardMarkdownDraft,
-    externalFocusNodeId,
-    externalFocusToken,
-    graphReady,
-    selectedNodeId,
-  ]);
+  }, [externalFocusNodeId, externalFocusToken, graphReady]);

  const handleEdgeSelect = useCallback((edgeId: string) => {
    setSelectedEdgeId(edgeId);
@@ -1878,37 +1843,6 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
    document.body.removeChild(anchor);
  }, [inspectableNodeId]);

-  const handleMarkdownApplied = useCallback((result: MarkdownApplyResult) => {
-    if (result.resource.kind !== "context-node") return;
-    if (!graph.hasNode(result.resource.id)) return;
-    const syncGeneration = markdownRefreshGuard.begin(result.resource.id);
-    const attributes = graph.getNodeAttributes(result.resource.id) as NodeAttributes;
-    graph.mergeNodeAttributes(
-      result.resource.id,
-      buildNodeMarkdownAttributeUpdate(
-        result.resource.id,
-        result.body,
-        attributes.properties ?? {},
-      ),
-    );
-    setGraphVersion((current) => current + 1);
-    sceneRef.current?.getRuntime()?.requestRender();
-
-    void readNodeMarkdownAttributeUpdate(result.resource.id)
-      .then((savedAttributes) => {
-        if (
-          !markdownRefreshGuard.isCurrent(result.resource.id, syncGeneration)
-          || !graph.hasNode(result.resource.id)
-        ) return;
-        graph.mergeNodeAttributes(result.resource.id, savedAttributes);
-        setGraphVersion((current) => current + 1);
-        sceneRef.current?.getRuntime()?.requestRender();
-      })
-      .catch((syncError) => {
-        console.error("[GraphWorkspace] applied node refresh failed", syncError);
-      });
-  }, [markdownRefreshGuard]);
-
  useEffect(() => {
    const protocol = window.location.protocol === "https:" ? "wss:" : "ws:";
    const socket = new WebSocket(`${protocol}//${window.location.host}/ws/graph-updates`);
@@ -1939,25 +1873,6 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
          setGraphVersion((current) => current + 1);
          sceneRef.current?.getRuntime()?.requestRender();
        }
-        if (eventType === "UPDATE_NODE" && payload?.id && graph.hasNode(payload.id)) {
-          markdownRefreshGuard.invalidate(payload.id);
-          const properties = payload.properties ?? {};
-          const current = graph.getNodeAttributes(payload.id) as NodeAttributes;
-          const content = typeof properties.content === "string" ? properties.content : "";
-          graph.mergeNodeAttributes(payload.id, {
-            ...buildNodeMarkdownAttributeUpdate(payload.id, content, properties),
-            nodeType: payload.type ?? current.nodeType,
-            valid_from: properties.valid_from ?? null,
-            valid_until: properties.valid_until ?? null,
-          });
-          logEvent(
-            "update-node",
-            `Updated node ${payload.id} via realtime ws`,
-            { nodeId: payload.id, nodeType: payload.type },
-          );
-          setGraphVersion((version) => version + 1);
-          sceneRef.current?.getRuntime()?.requestRender();
-        }
        if (eventType === "ADD_EDGE") {
          const isSmallGraph = smallGraphModeRef.current;
          batchMergeEdges([
@@ -1984,7 +1899,7 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
    return () => {
      socket.close();
    };
-  }, [markdownRefreshGuard]);
+  }, []);

  useEffect(() => {
    setCollapsedNeighborhoodNodeIds([]);
@@ -2257,29 +2172,28 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
  }, [collapsedNeighborhoodNodeIds, focusedNodeId, selectedNodeId, viewMode]);
  const structuralActivePath = structuralSelectedNodeId ? activePath : EMPTY_PATH;
  const structuralActivePathEdgeIds = structuralSelectedNodeId ? activePathEdgeIds : EMPTY_PATH;
-  const displayResult = useMemo(() => {
-    // The displayed graph is an aggregated clone. Rebuild it after domain
-    // mutations so applied Markdown labels do not remain stale on the canvas.
-    void graphVersion;
-    return viewMode === "grouped"
-      ? (groupedDisplayCandidate ?? resolveDisplayGraph("", EMPTY_PATH, EMPTY_PATH, "grouped", {
-          aggregationEnabled,
-          collapsedNeighborhoodNodeIds,
-        }))
-      : resolveDisplayGraph(structuralSelectedNodeId, structuralActivePath, structuralActivePathEdgeIds, viewMode, {
-          aggregationEnabled,
-          collapsedNeighborhoodNodeIds,
-        });
-  }, [
-    aggregationEnabled,
-    collapsedNeighborhoodNodeIds,
-    graphVersion,
-    groupedDisplayCandidate,
-    structuralActivePath,
-    structuralActivePathEdgeIds,
-    structuralSelectedNodeId,
-    viewMode,
-  ]);
+  const displayResult = useMemo(
+    () => (
+      viewMode === "grouped"
+        ? (groupedDisplayCandidate ?? resolveDisplayGraph("", EMPTY_PATH, EMPTY_PATH, "grouped", {
+            aggregationEnabled,
+            collapsedNeighborhoodNodeIds,
+          }))
+        : resolveDisplayGraph(structuralSelectedNodeId, structuralActivePath, structuralActivePathEdgeIds, viewMode, {
+            aggregationEnabled,
+            collapsedNeighborhoodNodeIds,
+          })
+    ),
+    [
+      aggregationEnabled,
+      collapsedNeighborhoodNodeIds,
+      groupedDisplayCandidate,
+      structuralActivePath,
+      structuralActivePathEdgeIds,
+      structuralSelectedNodeId,
+      viewMode,
+    ],
+  );
  const displayState = useMemo(
    () => (
      viewMode === "grouped"
@@ -3381,8 +3295,6 @@ export function GraphWorkspace({ externalFocusNodeId, externalFocusToken, onDirt
                      pathResult={pathResult}
                      onDownloadProvenance={(format) => void handleDownloadProvenance(format)}
                      onFocusNode={focusNode}
-                      onMarkdownApplied={handleMarkdownApplied}
-                      onMarkdownDirtyChange={handleMarkdownDirtyChange}
                    />
                  </Suspense>
                </div>
@@ -1,243 +1,125 @@
-import {
-  useEffect,
-  useMemo,
-  useRef,
-  useState,
-  type CSSProperties,
-} from "react";
+import { useState, useRef, useEffect, useMemo, type CSSProperties } from "react";
 import ReactMarkdown, { type Components } from "react-markdown";
 import remarkGfm from "remark-gfm";
-import {
-  Check,
-  Code2,
-  Copy,
-  Eye,
-  ExternalLink,
-  Image as ImageIcon,
-  Loader2,
-  Pencil,
-  RefreshCw,
-  X,
-} from "lucide-react";
+import { Check, Copy, Code2, Eye, ExternalLink, Image as ImageIcon } from "lucide-react";
 import { GRAPH_THEME } from "./graphTheme";
-import type { MarkdownApplyResult } from "./markdownResourceClient";
-import type { MarkdownResourceRef } from "./markdownEditorState";
 import { isSafeUrl } from "./markdownUrlSafety";
-import { useMarkdownEditor } from "./useMarkdownEditor";

 export interface MarkdownContentViewerProps {
  content?: string | null;
-  resource?: MarkdownResourceRef;
-  onApplied?: (result: MarkdownApplyResult) => void;
-  onDirtyChange?: (dirty: boolean) => void;
  className?: string;
  defaultMode?: "preview" | "source";
 }

 export function MarkdownContentViewer({
  content,
-  resource,
-  onApplied,
-  onDirtyChange,
  className,
  defaultMode = "preview",
 }: MarkdownContentViewerProps) {
  const [activeMode, setActiveMode] = useState<"preview" | "source">(defaultMode);
  const [copied, setCopied] = useState(false);
-  const modeBeforeEditRef = useRef<"preview" | "source">(defaultMode);
-  const resourceKey = resource ? `${resource.kind}:${resource.id}` : "";
-  const [activeResourceKey, setActiveResourceKey] = useState(resourceKey);
-  const editor = useMarkdownEditor({ resource, onApplied, onDirtyChange });
-  const {
-    session,
-    error,
-    dirty,
-    editing,
-    saving,
-    loading,
-  } = editor;
-
-  if (activeResourceKey !== resourceKey) {
-    setActiveResourceKey(resourceKey);
-    setCopied(false);
-    setActiveMode(defaultMode);
-  }
-
  // 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) setCopied(false);
+    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<number | undefined>(undefined);
+  const copyTimeoutRef = useRef<ReturnType<typeof setTimeout> | null>(null);
+
+  // Clean up any outstanding timeout on unmount.
  useEffect(() => {
    return () => {
-      clearTimeout(copyTimeoutRef.current);
+      if (copyTimeoutRef.current) {
+        clearTimeout(copyTimeoutRef.current);
+      }
    };
  }, []);

-  const rawContent = editor.editing
-    ? editor.session?.draft ?? ""
-    : (typeof content === "string" ? content : "");
-  const previewContent = useMemo(() => {
-    if (!editor.editing) return rawContent;
-    const lines = rawContent.split(/\r?\n/);
-    if (lines[0] !== "---") return rawContent;
-    const closingIndex = lines.findIndex((line, index) => index > 0 && line === "---");
-    return closingIndex < 0 ? rawContent : lines.slice(closingIndex + 1).join("\n").replace(/^\n/, "");
-  }, [editor.editing, rawContent]);
+  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}>
-        {previewContent}
+        {rawContent}
      </ReactMarkdown>
    ),
-    [previewContent],
+    [rawContent],
  );
+
  const handleCopy = async () => {
    if (!hasContent) return;
    try {
      await navigator.clipboard.writeText(rawContent);
-      clearTimeout(copyTimeoutRef.current);
+      if (copyTimeoutRef.current) {
+        clearTimeout(copyTimeoutRef.current);
+      }
      setCopied(true);
-      copyTimeoutRef.current = window.setTimeout(() => setCopied(false), 1500);
+      copyTimeoutRef.current = setTimeout(() => setCopied(false), 1500);
    } catch {
-      // Clipboard write unavailable.
-    }
-  };
-
-  const handleEdit = async () => {
-    modeBeforeEditRef.current = activeMode;
-    setActiveMode("source");
-    if (!await editor.beginEdit()) {
-      setActiveMode(modeBeforeEditRef.current);
-    }
-  };
-
-  const handleCancel = () => {
-    editor.discard();
-    setActiveMode(modeBeforeEditRef.current);
-  };
-
-  const handleApply = async () => {
-    if (await editor.save()) {
-      setActiveMode("preview");
+      // Clipboard write unavailable
    }
  };

  return (
    <div className={className} style={viewerContainerStyle}>
      <div style={viewerHeaderStyle}>
-        <div style={{ display: "flex", gap: 4 }} role="tablist" aria-label="Markdown view">
+        <div style={{ display: "flex", gap: 4 }} role="tablist">
          <button
            type="button"
            role="tab"
            aria-selected={activeMode === "preview"}
-            aria-controls="markdown-viewer-panel"
            onClick={() => setActiveMode("preview")}
            style={{ ...tabBtnStyle, ...(activeMode === "preview" ? activeTabBtnStyle : {}) }}
          >
-            <Eye size={12} style={{ marginRight: 5 }} aria-hidden="true" />
+            <Eye size={12} style={{ marginRight: 5 }} />
            Preview
          </button>
          <button
            type="button"
            role="tab"
            aria-selected={activeMode === "source"}
-            aria-controls="markdown-viewer-panel"
            onClick={() => setActiveMode("source")}
            style={{ ...tabBtnStyle, ...(activeMode === "source" ? activeTabBtnStyle : {}) }}
          >
-            <Code2 size={12} style={{ marginRight: 5 }} aria-hidden="true" />
+            <Code2 size={12} style={{ marginRight: 5 }} />
            Source
          </button>
        </div>

-        <div style={{ display: "flex", alignItems: "center", gap: 6 }}>
-          {hasContent && (
-            <button type="button" onClick={() => void handleCopy()} style={copyBtnStyle} title="Copy raw content">
-              {copied ? (
-                <>
-                  <Check size={12} color="#3fb950" style={{ marginRight: 4 }} aria-hidden="true" />
-                  <span style={{ color: "#3fb950", fontSize: 11 }}>Copied</span>
-                </>
-              ) : (
-                <>
-                  <Copy size={12} style={{ marginRight: 4 }} aria-hidden="true" />
-                  <span style={{ fontSize: 11 }}>Copy</span>
-                </>
-              )}
-            </button>
-          )}
-          {resource && !editing && !loading ? (
-            <button type="button" onClick={() => void handleEdit()} style={copyBtnStyle}>
-              <Pencil size={12} style={{ marginRight: 4 }} aria-hidden="true" />
-              Edit
-            </button>
-          ) : null}
-          {loading ? (
-            <button type="button" disabled style={{ ...copyBtnStyle, opacity: 0.65 }}>
-              <Loader2 size={12} className="animate-spin" style={{ marginRight: 4 }} aria-hidden="true" />
-              Loading…
-            </button>
-          ) : null}
-          {editing ? (
-            <>
-              <button type="button" onClick={handleCancel} disabled={saving} style={copyBtnStyle}>
-                <X size={12} style={{ marginRight: 4 }} aria-hidden="true" />
-                Cancel
-              </button>
-              <button
-                type="button"
-                onClick={() => void handleApply()}
-                disabled={saving || !dirty}
-                title={!dirty ? "Make a change before applying" : undefined}
-                style={{ ...saveBtnStyle, opacity: saving || !dirty ? 0.55 : 1 }}
-              >
-                {saving ? (
-                  <Loader2 size={12} className="animate-spin" style={{ marginRight: 4 }} aria-hidden="true" />
-                ) : (
-                  <Check size={12} style={{ marginRight: 4 }} aria-hidden="true" />
-                )}
-                {saving ? "Applying…" : "Apply"}
-              </button>
-            </>
-          ) : null}
-        </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>

-      {error ? (
-        <div id="markdown-editor-error" role="alert" style={errorStyle}>
-          <span>{error.message}</span>
-          {error.kind === "conflict" ? (
-            <button type="button" onClick={() => void editor.reloadLatest()} style={errorActionStyle}>
-              <RefreshCw size={12} style={{ marginRight: 4 }} aria-hidden="true" />
-              Reload latest
-            </button>
-          ) : null}
-        </div>
-      ) : null}
-
-      <div
-        id="markdown-viewer-panel"
-        role="tabpanel"
-        aria-busy={saving || loading}
-        style={viewerBodyStyle}
-      >
-        {activeMode === "source" && editing ? (
-          <textarea
-            aria-label="Markdown source"
-            aria-describedby={error ? "markdown-editor-error" : undefined}
-            aria-invalid={error?.kind === "validation" || undefined}
-            value={session?.draft ?? ""}
-            onChange={(event) => editor.changeDraft(event.target.value)}
-            disabled={saving}
-            spellCheck={false}
-            style={editorStyle}
-          />
-        ) : !hasContent ? (
+      <div style={viewerBodyStyle}>
+        {!hasContent ? (
          <div style={emptyTextStyle}>No content available for this node.</div>
        ) : activeMode === "source" ? (
          <pre style={sourcePreStyle}>
@@ -356,8 +238,6 @@ const viewerHeaderStyle: CSSProperties = {
  display: "flex",
  alignItems: "center",
  justifyContent: "space-between",
-  gap: 8,
-  flexWrap: "wrap",
  padding: "6px 10px",
  background: "rgba(0, 0, 0, 0.2)",
  borderBottom: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
@@ -395,56 +275,12 @@ const copyBtnStyle: CSSProperties = {
  cursor: "pointer",
 };

-const saveBtnStyle: CSSProperties = {
-  ...copyBtnStyle,
-  background: GRAPH_THEME.ui.control.primaryBg,
-  border: `1px solid ${GRAPH_THEME.ui.control.primaryBorder}`,
-  color: GRAPH_THEME.ui.control.primaryText,
-  fontWeight: 700,
-};
-
-const errorStyle: CSSProperties = {
-  display: "flex",
-  alignItems: "center",
-  justifyContent: "space-between",
-  gap: 8,
-  padding: "8px 12px",
-  color: "#ffb4ad",
-  background: "rgba(248, 81, 73, 0.1)",
-  borderBottom: "1px solid rgba(248, 81, 73, 0.25)",
-  fontSize: 12,
-  lineHeight: 1.5,
-};
-
-const errorActionStyle: CSSProperties = {
-  ...copyBtnStyle,
-  flexShrink: 0,
-  color: "#ffb4ad",
-  border: "1px solid rgba(248, 81, 73, 0.32)",
-};
-
 const viewerBodyStyle: CSSProperties = {
  padding: 12,
  maxHeight: 380,
  overflowY: "auto",
 };

-const editorStyle: CSSProperties = {
-  display: "block",
-  boxSizing: "border-box",
-  width: "100%",
-  minHeight: 280,
-  resize: "vertical",
-  padding: 10,
-  borderRadius: 8,
-  border: `1px solid ${GRAPH_THEME.ui.control.activeBorder}`,
-  background: "rgba(0, 0, 0, 0.3)",
-  color: GRAPH_THEME.ui.text.strong,
-  fontFamily: "'JetBrains Mono', 'Fira Code', monospace",
-  fontSize: 12,
-  lineHeight: 1.6,
-};
-
 const emptyTextStyle: CSSProperties = {
  color: GRAPH_THEME.ui.text.muted,
  fontSize: 12,
@@ -1,114 +0,0 @@
-export type MarkdownResourceRef =
-  | { kind: "context-node"; id: string }
-  | { kind: "agent-memory"; id: string };
-
-export type EditorStatus =
-  | "viewing"
-  | "loading-document"
-  | "editing"
-  | "saving"
-  | "validation-error"
-  | "save-error"
-  | "conflict";
-
-export interface MarkdownEditorError {
-  kind: "validation" | "conflict" | "save" | "network";
-  message: string;
-  field?: string;
-  currentRevision?: string;
-}
-
-export interface MarkdownEditSession {
-  resource: MarkdownResourceRef;
-  baseSource: string;
-  baseRevision: string;
-  draft: string;
-  status: EditorStatus;
-  error: MarkdownEditorError | null;
-}
-
-export interface MarkdownSavedDocument {
-  source: string;
-  revision: string;
-}
-
-export function createLoadingSession(resource: MarkdownResourceRef): MarkdownEditSession {
-  return {
-    resource,
-    baseSource: "",
-    baseRevision: "",
-    draft: "",
-    status: "loading-document",
-    error: null,
-  };
-}
-
-export function createEditSession(
-  resource: MarkdownResourceRef,
-  document: MarkdownSavedDocument,
-): MarkdownEditSession {
-  return {
-    resource,
-    baseSource: document.source,
-    baseRevision: document.revision,
-    draft: document.source,
-    status: "editing",
-    error: null,
-  };
-}
-
-export function updateDraft(
-  session: MarkdownEditSession,
-  draft: string,
-): MarkdownEditSession {
-  return {
-    ...session,
-    draft,
-    status: "editing",
-    error: null,
-  };
-}
-
-export function isDirty(session: MarkdownEditSession | null): boolean {
-  return session !== null && session.draft !== session.baseSource;
-}
-
-export function saveStarted(session: MarkdownEditSession): MarkdownEditSession {
-  if (!isDirty(session)) return session;
-  return { ...session, status: "saving", error: null };
-}
-
-export function saveSucceeded(
-  session: MarkdownEditSession,
-  document: MarkdownSavedDocument,
-): MarkdownEditSession {
-  return {
-    ...session,
-    baseSource: document.source,
-    baseRevision: document.revision,
-    draft: document.source,
-    status: "viewing",
-    error: null,
-  };
-}
-
-export function saveFailed(
-  session: MarkdownEditSession,
-  error: MarkdownEditorError,
-): MarkdownEditSession {
-  const status: EditorStatus =
-    error.kind === "validation"
-      ? "validation-error"
-      : error.kind === "conflict"
-        ? "conflict"
-        : "save-error";
-  return { ...session, status, error };
-}
-
-export function cancelEdit(): null {
-  return null;
-}
-
-export function shouldConfirmDiscard(session: MarkdownEditSession | null): boolean {
-  return isDirty(session) && session?.status !== "saving";
-}
@@ -1,103 +0,0 @@
-import type {
-  MarkdownEditorError,
-  MarkdownResourceRef,
-} from "./markdownEditorState";
-
-export interface MarkdownDocument {
-  resource: MarkdownResourceRef;
-  source: string;
-  body: string;
-  revision: string;
-  editable: boolean;
-}
-
-export interface MarkdownApplyResult extends MarkdownDocument {
-  changed: boolean;
-}
-
-type ErrorDetail = {
-  code?: string;
-  message?: string;
-  field?: string;
-  current_revision?: string;
-};
-
-export class MarkdownClientError extends Error implements MarkdownEditorError {
-  readonly kind: MarkdownEditorError["kind"];
-  readonly field?: string;
-  readonly currentRevision?: string;
-
-  constructor(error: MarkdownEditorError) {
-    super(error.message);
-    this.name = "MarkdownClientError";
-    this.kind = error.kind;
-    this.field = error.field;
-    this.currentRevision = error.currentRevision;
-  }
-}
-
-function resourceUrl(ref: MarkdownResourceRef): string {
-  return `/api/markdown/${ref.kind}/${encodeURIComponent(ref.id)}`;
-}
-
-async function responseError(response: Response): Promise<MarkdownClientError> {
-  let detail: ErrorDetail = {};
-  try {
-    const payload = (await response.json()) as { detail?: ErrorDetail };
-    if (payload.detail && typeof payload.detail === "object") {
-      detail = payload.detail;
-    }
-  } catch {
-    // A non-JSON response is mapped from its status below.
-  }
-
-  const kind: MarkdownEditorError["kind"] =
-    response.status === 422
-      ? "validation"
-      : response.status === 409
-        ? "conflict"
-        : "save";
-  return new MarkdownClientError({
-    kind,
-    message: detail.message || `Markdown request failed (${response.status}).`,
-    field: detail.field,
-    currentRevision: detail.current_revision,
-  });
-}
-
-async function request<T>(input: RequestInfo | URL, init?: RequestInit): Promise<T> {
-  try {
-    const response = await fetch(input, init);
-    if (!response.ok) {
-      throw await responseError(response);
-    }
-    return (await response.json()) as T;
-  } catch (error) {
-    if (error instanceof MarkdownClientError) throw error;
-    throw new MarkdownClientError({
-      kind: "network",
-      message: "The Markdown service could not be reached. Your draft was kept.",
-    });
-  }
-}
-
-export function readMarkdownResource(
-  ref: MarkdownResourceRef,
-): Promise<MarkdownDocument> {
-  return request<MarkdownDocument>(resourceUrl(ref));
-}
-
-export function applyMarkdownResource(
-  ref: MarkdownResourceRef,
-  markdown: string,
-  expectedRevision: string,
-): Promise<MarkdownApplyResult> {
-  return request<MarkdownApplyResult>(resourceUrl(ref), {
-    method: "PUT",
-    headers: { "Content-Type": "application/json" },
-    body: JSON.stringify({
-      markdown,
-      expected_revision: expectedRevision,
-    }),
-  });
-}
@@ -1,81 +0,0 @@
-export interface NodeMarkdownAttributeUpdate {
-  label: string;
-  content: string;
-  properties: Record<string, unknown>;
-}
-
-export interface GraphNodeMarkdownSnapshot {
-  id: string;
-  type: string;
-  content: string;
-  properties: Record<string, unknown>;
-  valid_from: string | null;
-  valid_until: string | null;
-}
-
-export interface SavedNodeMarkdownAttributeUpdate extends NodeMarkdownAttributeUpdate {
-  nodeType: string;
-  valid_from: string | null;
-  valid_until: string | null;
-}
-
-export class NodeMarkdownRefreshGuard {
-  private readonly generations = new Map<string, number>();
-
-  begin(nodeId: string): number {
-    const generation = (this.generations.get(nodeId) ?? 0) + 1;
-    this.generations.set(nodeId, generation);
-    return generation;
-  }
-
-  invalidate(nodeId: string): void {
-    this.begin(nodeId);
-  }
-
-  isCurrent(nodeId: string, generation: number): boolean {
-    return this.generations.get(nodeId) === generation;
-  }
-}
-
-export function buildNodeMarkdownAttributeUpdate(
-  nodeId: string,
-  content: string,
-  properties: Record<string, unknown>,
-): NodeMarkdownAttributeUpdate {
-  return {
-    label: content || nodeId,
-    content,
-    properties: {
-      ...properties,
-      content,
-    },
-  };
-}
-
-export async function readNodeMarkdownAttributeUpdate(
-  nodeId: string,
-  fetcher: typeof fetch = fetch,
-): Promise<SavedNodeMarkdownAttributeUpdate> {
-  const response = await fetcher(
-    `/api/graph/node?node_id=${encodeURIComponent(nodeId)}`,
-  );
-  if (!response.ok) {
-    throw new Error(`Graph node refresh failed (${response.status}).`);
-  }
-
-  const node = await response.json() as GraphNodeMarkdownSnapshot;
-  if (node.id !== nodeId) {
-    throw new Error("Graph node refresh returned a different resource.");
-  }
-
-  return {
-    ...buildNodeMarkdownAttributeUpdate(
-      node.id,
-      node.content,
-      node.properties ?? {},
-    ),
-    nodeType: node.type,
-    valid_from: node.valid_from ?? null,
-    valid_until: node.valid_until ?? null,
-  };
-}
@@ -1,177 +0,0 @@
-import {
-  useCallback,
-  useEffect,
-  useLayoutEffect,
-  useRef,
-  useState,
-} from "react";
-import {
-  MarkdownClientError,
-  applyMarkdownResource,
-  readMarkdownResource,
-  type MarkdownApplyResult,
-} from "./markdownResourceClient";
-import {
-  cancelEdit,
-  createEditSession,
-  createLoadingSession,
-  isDirty,
-  saveFailed,
-  saveStarted,
-  saveSucceeded,
-  updateDraft,
-  type MarkdownEditorError,
-  type MarkdownEditSession,
-  type MarkdownResourceRef,
-} from "./markdownEditorState";
-
-interface MarkdownEditorOptions {
-  resource?: MarkdownResourceRef;
-  onApplied?: (result: MarkdownApplyResult) => void;
-  onDirtyChange?: (dirty: boolean) => void;
-}
-
-interface KeyedError {
-  resourceKey: string;
-  error: MarkdownEditorError;
-}
-
-function keyOf(resource?: MarkdownResourceRef): string {
-  return resource ? `${resource.kind}:${resource.id}` : "";
-}
-
-function normalizeError(failure: unknown): MarkdownEditorError {
-  if (failure instanceof MarkdownClientError) return failure;
-  return {
-    kind: "network",
-    message: "The Markdown service could not be reached. Your draft was kept.",
-  };
-}
-
-export function useMarkdownEditor({
-  resource,
-  onApplied,
-  onDirtyChange,
-}: MarkdownEditorOptions) {
-  const resourceKey = keyOf(resource);
-  const [session, setSession] = useState<MarkdownEditSession | null>(null);
-  const [viewError, setViewError] = useState<KeyedError | null>(null);
-  const [renderedResourceKey, setRenderedResourceKey] = useState(resourceKey);
-  const loadGenerationRef = useRef(0);
-
-  if (renderedResourceKey !== resourceKey) {
-    setRenderedResourceKey(resourceKey);
-    setSession(null);
-    setViewError(null);
-  }
-
-  useLayoutEffect(() => {
-    loadGenerationRef.current += 1;
-  }, [resourceKey]);
-
-  const activeSession = session && keyOf(session.resource) === resourceKey
-    ? session
-    : null;
-  const dirty = isDirty(activeSession);
-  const editing = activeSession !== null
-    && activeSession.status !== "viewing"
-    && activeSession.status !== "loading-document";
-  const saving = activeSession?.status === "saving";
-  const loading = activeSession?.status === "loading-document";
-  const error = activeSession?.error
-    ?? (viewError?.resourceKey === resourceKey ? viewError.error : null);
-
-  useEffect(() => {
-    onDirtyChange?.(dirty);
-    return () => {
-      if (dirty) onDirtyChange?.(false);
-    };
-  }, [dirty, onDirtyChange]);
-
-  useEffect(() => {
-    if (!dirty) return;
-    const protectDraft = (event: BeforeUnloadEvent) => {
-      event.preventDefault();
-      event.returnValue = "";
-    };
-    window.addEventListener("beforeunload", protectDraft);
-    return () => window.removeEventListener("beforeunload", protectDraft);
-  }, [dirty]);
-
-  const beginEdit = useCallback(async () => {
-    if (!resource) return false;
-    const loadGeneration = ++loadGenerationRef.current;
-    setViewError(null);
-    setSession(createLoadingSession(resource));
-    try {
-      const document = await readMarkdownResource(resource);
-      if (loadGeneration !== loadGenerationRef.current) return false;
-      setSession(createEditSession(resource, document));
-      return true;
-    } catch (failure) {
-      if (loadGeneration !== loadGenerationRef.current) return false;
-      setSession(null);
-      setViewError({ resourceKey, error: normalizeError(failure) });
-      return false;
-    }
-  }, [resource, resourceKey]);
-
-  const discard = useCallback(() => {
-    if (!activeSession || saving) return;
-    setSession(cancelEdit());
-    setViewError(null);
-  }, [activeSession, saving]);
-
-  const save = useCallback(async () => {
-    if (!activeSession || saving || !dirty) return false;
-    const resourceGeneration = loadGenerationRef.current;
-    const pending = saveStarted(activeSession);
-    setSession(pending);
-    try {
-      const result = await applyMarkdownResource(
-        pending.resource,
-        pending.draft,
-        pending.baseRevision,
-      );
-      if (resourceGeneration !== loadGenerationRef.current) return false;
-      setSession(saveSucceeded(pending, result));
-      onApplied?.(result);
-      return true;
-    } catch (failure) {
-      if (resourceGeneration !== loadGenerationRef.current) return false;
-      setSession(saveFailed(pending, normalizeError(failure)));
-      return false;
-    }
-  }, [activeSession, dirty, onApplied, saving]);
-
-  const reloadLatest = useCallback(async () => {
-    if (!resource || saving) return;
-    if (
-      dirty
-      && !window.confirm("Discard this draft and reload the latest applied version?")
-    ) return;
-    await beginEdit();
-  }, [beginEdit, dirty, resource, saving]);
-
-  const changeDraft = useCallback((draft: string) => {
-    setSession((current) => (
-      current && keyOf(current.resource) === resourceKey
-        ? updateDraft(current, draft)
-        : current
-    ));
-  }, [resourceKey]);
-
-  return {
-    session: activeSession,
-    error,
-    dirty,
-    editing,
-    saving,
-    loading,
-    beginEdit,
-    discard,
-    save,
-    reloadLatest,
-    changeDraft,
-  };
-}
@@ -1,464 +0,0 @@
-import { useCallback, useEffect, useRef, useState, type CSSProperties } from "react";
-import { Brain, RefreshCw } from "lucide-react";
-
-import { MarkdownContentViewer } from "./GraphWorkspace/MarkdownContentViewer";
-import {
-  readMarkdownResource,
-  type MarkdownApplyResult,
-} from "./GraphWorkspace/markdownResourceClient";
-import { GRAPH_THEME } from "./GraphWorkspace/graphTheme";
-
-interface MemorySummary {
-  id: string;
-  type: string;
-  excerpt: string;
-  updated_at: string | null;
-}
-
-interface MemoryListResponse {
-  items: MemorySummary[];
-  total: number;
-  skip: number;
-  limit: number;
-}
-interface MemoryWorkspaceProps {
-  onDirtyChange?: (dirty: boolean) => void;
-}
-
-const MEMORY_PAGE_SIZE = 100;
-
-
-function responseMessage(payload: unknown, fallback: string): string {
-  if (!payload || typeof payload !== "object" || !("detail" in payload)) {
-    return fallback;
-  }
-  return typeof payload.detail === "string" ? payload.detail : fallback;
-}
-
-
-async function fetchMemoryList(skip = 0): Promise<MemoryListResponse> {
-  const response = await fetch(`/api/memories?skip=${skip}&limit=${MEMORY_PAGE_SIZE}`);
-  if (!response.ok) {
-    const payload = await response.json().catch(() => null);
-    throw new Error(responseMessage(payload, `Memory list failed (${response.status}).`));
-  }
-  return response.json() as Promise<MemoryListResponse>;
-}
-
-async function fetchLoadedMemoryPages(endOffset: number): Promise<{
-  items: MemorySummary[];
-  total: number;
-  nextOffset: number;
-}> {
-  const items: MemorySummary[] = [];
-  let total = 0;
-  let nextOffset = 0;
-  const targetOffset = Math.max(endOffset, MEMORY_PAGE_SIZE);
-
-  while (nextOffset < targetOffset) {
-    const payload = await fetchMemoryList(nextOffset);
-    items.push(...payload.items);
-    total = payload.total;
-    nextOffset = payload.skip + payload.items.length;
-    if (payload.items.length === 0 || nextOffset >= total) break;
-  }
-
-  return { items, total, nextOffset };
-}
-
-export function MemoryWorkspace({ onDirtyChange }: MemoryWorkspaceProps = {}) {
-  const [items, setItems] = useState<MemorySummary[]>([]);
-  const [total, setTotal] = useState(0);
-  const [nextOffset, setNextOffset] = useState(0);
-  const [selectedId, setSelectedId] = useState("");
-  const [selectedBody, setSelectedBody] = useState("");
-  const [loading, setLoading] = useState(true);
-  const [loadingMore, setLoadingMore] = useState(false);
-  const [error, setError] = useState("");
-  const [dirty, setDirty] = useState(false);
-  const [reloadToken, setReloadToken] = useState(0);
-  const listGenerationRef = useRef(0);
-  const selectionGenerationRef = useRef(0);
-  const handleDirtyChange = useCallback((nextDirty: boolean) => {
-    setDirty(nextDirty);
-    onDirtyChange?.(nextDirty);
-  }, [onDirtyChange]);
-
-
-  useEffect(() => {
-    let cancelled = false;
-    const listGeneration = ++listGenerationRef.current;
-    const selectionGeneration = ++selectionGenerationRef.current;
-    const isCurrent = () => (
-      !cancelled
-      && listGeneration === listGenerationRef.current
-      && selectionGeneration === selectionGenerationRef.current
-    );
-    const load = async () => {
-      setLoading(true);
-      setLoadingMore(false);
-      setError("");
-      try {
-        const payload = await fetchMemoryList();
-        if (!isCurrent()) return;
-        setItems(payload.items);
-        setTotal(payload.total);
-        setNextOffset(payload.skip + payload.items.length);
-        const first = payload.items[0];
-        if (!first) {
-          setSelectedId("");
-          setSelectedBody("");
-          return;
-        }
-        const document = await readMarkdownResource({
-          kind: "agent-memory",
-          id: first.id,
-        });
-        if (!isCurrent()) return;
-        setSelectedId(first.id);
-        setSelectedBody(document.body);
-      } catch (failure) {
-        if (isCurrent()) {
-          setError(failure instanceof Error ? failure.message : "Memories could not be loaded.");
-        }
-      } finally {
-        if (isCurrent()) setLoading(false);
-      }
-    };
-    void load();
-    return () => {
-      cancelled = true;
-      listGenerationRef.current += 1;
-      selectionGenerationRef.current += 1;
-    };
-  }, [reloadToken]);
-
-  const selectMemory = async (memoryId: string) => {
-    if (memoryId === selectedId) return;
-    if (dirty && !window.confirm("Discard the unapplied Markdown draft and open another memory?")) return;
-    const selectionGeneration = ++selectionGenerationRef.current;
-    // Do NOT call handleDirtyChange(false) here: the editor's own onDirtyChange
-    // callback fires automatically when MarkdownContentViewer re-renders with
-    // the new resource prop and its session is cleared.
-    setLoading(true);
-    setError("");
-    try {
-      const document = await readMarkdownResource({
-        kind: "agent-memory",
-        id: memoryId,
-      });
-      if (selectionGeneration !== selectionGenerationRef.current) return;
-      setSelectedId(memoryId);
-      setSelectedBody(document.body);
-    } catch (failure) {
-      if (selectionGeneration === selectionGenerationRef.current) {
-        setError(failure instanceof Error ? failure.message : "The memory could not be loaded.");
-      }
-    } finally {
-      if (selectionGeneration === selectionGenerationRef.current) {
-        setLoading(false);
-      }
-    }
-  };
-
-  const loadMoreMemories = useCallback(async () => {
-    if (loadingMore || nextOffset >= total) return;
-    const listGeneration = ++listGenerationRef.current;
-    setLoadingMore(true);
-    setError("");
-    try {
-      const payload = await fetchMemoryList(nextOffset);
-      if (listGeneration !== listGenerationRef.current) return;
-      setItems((current) => {
-        const knownIds = new Set(current.map((item) => item.id));
-        return [
-          ...current,
-          ...payload.items.filter((item) => !knownIds.has(item.id)),
-        ];
-      });
-      setTotal(payload.total);
-      setNextOffset(payload.skip + payload.items.length);
-    } catch (failure) {
-      if (listGeneration === listGenerationRef.current) {
-        setError(failure instanceof Error ? failure.message : "More memories could not be loaded.");
-      }
-    } finally {
-      if (listGeneration === listGenerationRef.current) {
-        setLoadingMore(false);
-      }
-    }
-  }, [loadingMore, nextOffset, total]);
-
-  const refreshMemorySummaries = useCallback(async () => {
-    const listGeneration = ++listGenerationRef.current;
-    try {
-      const payload = await fetchLoadedMemoryPages(nextOffset);
-      if (listGeneration !== listGenerationRef.current) return;
-      setItems(payload.items);
-      setTotal(payload.total);
-      setNextOffset(payload.nextOffset);
-    } catch {
-      if (listGeneration === listGenerationRef.current) {
-        setError("Memory was applied, but its summary could not be refreshed.");
-      }
-    } finally {
-      if (listGeneration === listGenerationRef.current) {
-        setLoadingMore(false);
-      }
-    }
-  }, [nextOffset]);
-
-  const applyMemory = useCallback((result: MarkdownApplyResult) => {
-    setSelectedBody(result.body);
-    handleDirtyChange(false);
-    setItems((current) => current.map((item) => (
-      item.id === result.resource.id
-        ? { ...item, excerpt: result.body.replace(/\s+/g, " ").slice(0, 160) }
-        : item
-    )));
-    void refreshMemorySummaries();
-  }, [handleDirtyChange, refreshMemorySummaries]);
-
-  return (
-    <div style={workspaceStyle}>
-      <aside style={listPanelStyle} aria-label="Agent memories">
-        <div style={listHeaderStyle}>
-          <div>
-            <div style={listTitleStyle}>AgentMemory</div>
-            <div style={listCountStyle}>{items.length} of {total} loaded</div>
-          </div>
-          <button
-            type="button"
-            aria-label="Refresh memories"
-            onClick={() => setReloadToken((value) => value + 1)}
-            disabled={loading || loadingMore || dirty}
-            title={dirty ? "Apply or cancel the current draft before refreshing" : "Refresh memories"}
-            style={{ ...iconButtonStyle, opacity: loading || loadingMore || dirty ? 0.55 : 1 }}
-          >
-            <RefreshCw size={14} aria-hidden="true" />
-          </button>
-        </div>
-        <div style={memoryListStyle}>
-          {items.map((item) => (
-            <button
-              type="button"
-              key={item.id}
-              onClick={() => void selectMemory(item.id)}
-              aria-current={item.id === selectedId ? "true" : undefined}
-              style={{
-                ...memoryButtonStyle,
-                ...(item.id === selectedId ? selectedMemoryButtonStyle : {}),
-              }}
-            >
-              <span style={memoryTypeStyle}>{item.type}</span>
-              <span style={memoryIdStyle}>{item.id}</span>
-              <span style={memoryExcerptStyle}>{item.excerpt || "Empty memory"}</span>
-            </button>
-          ))}
-          {nextOffset < total ? (
-            <button
-              type="button"
-              aria-label="Load more memories"
-              onClick={() => void loadMoreMemories()}
-              disabled={loading || loadingMore}
-              style={{ ...retryButtonStyle, opacity: loading || loadingMore ? 0.55 : 1 }}
-            >
-              {loadingMore ? "Loading…" : "Load more"}
-            </button>
-          ) : null}
-          {!loading && items.length === 0 ? (
-            <div style={emptyStyle}>
-              <Brain size={22} aria-hidden="true" />
-              <span>No AgentMemory items are available.</span>
-              <button type="button" onClick={() => setReloadToken((value) => value + 1)} style={retryButtonStyle}>
-                Refresh
-              </button>
-            </div>
-          ) : null}
-        </div>
-      </aside>
-
-      <main style={editorPanelStyle}>
-        {error ? <div role="alert" style={alertStyle}>{error}</div> : null}
-        {loading ? (
-          <div role="status" style={emptyStyle}>Loading memories…</div>
-        ) : selectedId ? (
-          <>
-            <div style={selectionHeaderStyle}>
-              <span style={selectionLabelStyle}>Selected memory</span>
-              <strong style={selectionIdStyle}>{selectedId}</strong>
-            </div>
-            <MarkdownContentViewer
-              content={selectedBody}
-              resource={{ kind: "agent-memory", id: selectedId }}
-              onApplied={applyMemory}
-              onDirtyChange={handleDirtyChange}
-            />
-          </>
-        ) : null}
-      </main>
-    </div>
-  );
-}
-
-const workspaceStyle: CSSProperties = {
-  display: "grid",
-  gridTemplateColumns: "minmax(220px, 300px) minmax(0, 1fr)",
-  height: "100%",
-  minHeight: 0,
-  background: GRAPH_THEME.ui.surface.stage,
-};
-
-const listPanelStyle: CSSProperties = {
-  display: "flex",
-  flexDirection: "column",
-  minHeight: 0,
-  borderRight: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
-  background: GRAPH_THEME.ui.surface.panel,
-};
-
-const listHeaderStyle: CSSProperties = {
-  display: "flex",
-  alignItems: "center",
-  justifyContent: "space-between",
-  gap: 12,
-  padding: 16,
-  borderBottom: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
-};
-
-const listTitleStyle: CSSProperties = {
-  color: GRAPH_THEME.ui.text.strong,
-  fontSize: 14,
-  fontWeight: 700,
-};
-
-const listCountStyle: CSSProperties = {
-  color: GRAPH_THEME.ui.text.muted,
-  fontSize: 11,
-  marginTop: 3,
-};
-
-const iconButtonStyle: CSSProperties = {
-  display: "inline-grid",
-  placeItems: "center",
-  width: 30,
-  height: 30,
-  borderRadius: 8,
-  border: `1px solid ${GRAPH_THEME.ui.surface.panelBorder}`,
-  background: "rgba(255, 255, 255, 0.04)",
-  color: GRAPH_THEME.ui.text.body,
-  cursor: "pointer",
-};
-
-const memoryListStyle: CSSProperties = {
-  display: "flex",
-  flexDirection: "column",
-  gap: 6,
-  minHeight: 0,
-  padding: 10,
-  overflowY: "auto",
-};
-
-const memoryButtonStyle: CSSProperties = {
-  display: "flex",
-  flexDirection: "column",
-  alignItems: "flex-start",
-  gap: 5,
-  padding: 10,
-  borderRadius: 9,
-  border: "1px solid transparent",
-  background: "transparent",
-  color: GRAPH_THEME.ui.text.body,
-  textAlign: "left",
-  cursor: "pointer",
-};
-
-const selectedMemoryButtonStyle: CSSProperties = {
-  border: `1px solid ${GRAPH_THEME.ui.control.activeBorder}`,
-  background: GRAPH_THEME.ui.timeline.playheadSoft,
-};
-
-const memoryTypeStyle: CSSProperties = {
-  color: GRAPH_THEME.ui.timeline.playhead,
-  fontSize: 10,
-  fontWeight: 700,
-  textTransform: "uppercase",
-};
-
-const memoryIdStyle: CSSProperties = {
-  maxWidth: "100%",
-  overflow: "hidden",
-  color: GRAPH_THEME.ui.text.strong,
-  fontFamily: "monospace",
-  fontSize: 12,
-  textOverflow: "ellipsis",
-  whiteSpace: "nowrap",
-};
-
-const memoryExcerptStyle: CSSProperties = {
-  display: "-webkit-box",
-  overflow: "hidden",
-  color: GRAPH_THEME.ui.text.muted,
-  fontSize: 11,
-  lineHeight: 1.45,
-  WebkitBoxOrient: "vertical",
-  WebkitLineClamp: 2,
-};
-
-const editorPanelStyle: CSSProperties = {
-  minWidth: 0,
-  minHeight: 0,
-  padding: 20,
-  overflowY: "auto",
-};
-
-const selectionHeaderStyle: CSSProperties = {
-  display: "flex",
-  flexDirection: "column",
-  gap: 4,
-  marginBottom: 12,
-};
-
-const selectionLabelStyle: CSSProperties = {
-  color: GRAPH_THEME.ui.text.muted,
-  fontSize: 11,
-};
-
-const selectionIdStyle: CSSProperties = {
-  color: GRAPH_THEME.ui.text.strong,
-  fontFamily: "monospace",
-  fontSize: 14,
-  wordBreak: "break-all",
-};
-
-const emptyStyle: CSSProperties = {
-  display: "flex",
-  flexDirection: "column",
-  alignItems: "center",
-  justifyContent: "center",
-  gap: 10,
-  minHeight: 160,
-  padding: 20,
-  color: GRAPH_THEME.ui.text.muted,
-  fontSize: 12,
-  textAlign: "center",
-};
-
-const retryButtonStyle: CSSProperties = {
-  padding: "6px 10px",
-  borderRadius: 7,
-  border: `1px solid ${GRAPH_THEME.ui.control.activeBorder}`,
-  background: GRAPH_THEME.ui.timeline.playheadSoft,
-  color: GRAPH_THEME.ui.timeline.playhead,
-  cursor: "pointer",
-};
-
-const alertStyle: CSSProperties = {
-  marginBottom: 12,
-  padding: "10px 12px",
-  borderRadius: 8,
-  border: "1px solid rgba(248, 81, 73, 0.28)",
-  background: "rgba(248, 81, 73, 0.1)",
-  color: "#ffb4ad",
-  fontSize: 12,
-};
@@ -42,9 +42,6 @@ async function startVite(): Promise<void> {
 }

 async function installApiFixture(page: Page): Promise<void> {
-  await page.route("**/api/info", async (route) => {
-    await route.fulfill({ json: { capabilities: { agent_memory: false } } });
-  });
  await page.route("**/api/graph/**", async (route) => {
    const pathname = new URL(route.request().url()).pathname;
    if (pathname === "/api/graph/stats") {
@@ -1,74 +0,0 @@
-import assert from "node:assert/strict";
-import test from "node:test";
-
-import { JSDOM } from "jsdom";
-import React from "react";
-
-import { fetchAgentMemoryAvailability } from "../src/explorerCapabilities.ts";
-
-(globalThis as typeof globalThis & { React: typeof React }).React = React;
-const dom = new JSDOM("<!doctype html><html><body></body></html>", {
-  url: "http://localhost",
-});
-Object.assign(globalThis, {
-  window: dom.window,
-  document: dom.window.document,
-  HTMLElement: dom.window.HTMLElement,
-  Node: dom.window.Node,
-});
-Object.defineProperty(globalThis, "navigator", {
-  configurable: true,
-  value: dom.window.navigator,
-});
-
-const { cleanup, render } = await import("@testing-library/react");
-const { ExploreWorkspaceTabs } = await import("../src/ExploreWorkspaceTabs.tsx");
-
-test.afterEach(cleanup);
-
-test("reports AgentMemory when the Explorer host provides it", async () => {
-  const available = await fetchAgentMemoryAvailability(async () => (
-    new Response(
-      JSON.stringify({ capabilities: { agent_memory: true } }),
-      { status: 200, headers: { "content-type": "application/json" } },
-    )
-  ));
-
-  assert.equal(available, true);
-});
-
-test("keeps AgentMemory hidden when the capability is absent or unavailable", async () => {
-  const absent = await fetchAgentMemoryAvailability(async () => (
-    new Response(JSON.stringify({ status: "active" }), { status: 200 })
-  ));
-  const unavailable = await fetchAgentMemoryAvailability(async () => {
-    throw new Error("network unavailable");
-  });
-
-  assert.equal(absent, false);
-  assert.equal(unavailable, false);
-});
-
-test("shows the Memories tab only when the host provides AgentMemory", () => {
-  const availableView = render(
-    <ExploreWorkspaceTabs
-      activeView="graph"
-      agentMemoryAvailable
-      onSelect={() => undefined}
-    />,
-  );
-  assert.ok(availableView.getByRole("button", { name: "Memories" }));
-  cleanup();
-
-  const unavailableView = render(
-    <ExploreWorkspaceTabs
-      activeView="graph"
-      agentMemoryAvailable={false}
-      onSelect={() => undefined}
-    />,
-  );
-  assert.equal(
-    unavailableView.queryByRole("button", { name: "Memories" }),
-    null,
-  );
-});
@@ -3,7 +3,7 @@ import assert from "node:assert/strict";
 import React from "react";
 import { renderToString } from "react-dom/server";

-(globalThis as typeof globalThis & { React: typeof React }).React = React;
+(globalThis as any).React = React;

 import { MarkdownContentViewer } from "../src/workspaces/GraphWorkspace/MarkdownContentViewer.tsx";
 import { isSafeUrl } from "../src/workspaces/GraphWorkspace/markdownUrlSafety.ts";
@@ -60,29 +60,6 @@ test("renders Preview mode with formatted Markdown elements and tabs", () => {
  assert.equal(html.includes("Item B"), true);
 });

-test("stays read-only without a resource and exposes Edit for canonical resources", () => {
-  const readOnly = renderToString(React.createElement(MarkdownContentViewer, {
-    content: "Read-only body",
-  }));
-  const editable = renderToString(React.createElement(MarkdownContentViewer, {
-    content: "Editable body",
-    resource: { kind: "context-node", id: "node-1" },
-  }));
-
-  assert.equal(readOnly.includes(">Edit</button>"), false);
-  assert.equal(editable.includes(">Edit</button>"), true);
-});
-
-test("empty canonical resources still expose Edit", () => {
-  const html = renderToString(React.createElement(MarkdownContentViewer, {
-    content: "",
-    resource: { kind: "context-node", id: "empty-node" },
-  }));
-
-  assert.equal(html.includes("No content available for this node."), true);
-  assert.equal(html.includes(">Edit</button>"), 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" }));
@@ -1,639 +0,0 @@
-import assert from "node:assert/strict";
-import test from "node:test";
-
-import { JSDOM } from "jsdom";
-import React from "react";
-
-(globalThis as typeof globalThis & { React: typeof React }).React = React;
-const dom = new JSDOM("<!doctype html><html><body></body></html>", {
-  url: "http://localhost",
-});
-Object.assign(globalThis, {
-  window: dom.window,
-  document: dom.window.document,
-  HTMLElement: dom.window.HTMLElement,
-  Node: dom.window.Node,
-});
-Object.defineProperty(globalThis, "navigator", {
-  configurable: true,
-  value: dom.window.navigator,
-});
-dom.window.confirm = () => true;
-
-// Testing Library and the components must load after the jsdom globals above.
-const { act, cleanup, fireEvent, render, waitFor } = await import(
-  "@testing-library/react"
-);
-const { MarkdownContentViewer } = await import(
-  "../src/workspaces/GraphWorkspace/MarkdownContentViewer.tsx"
-);
-const { MemoryWorkspace } = await import(
-  "../src/workspaces/MemoryWorkspace.tsx"
-);
-
-test.afterEach(() => {
-  cleanup();
-  dom.window.confirm = () => true;
-});
-
-const resource = { kind: "context-node" as const, id: "node-1" };
-const originalSource = "---\nid: node-1\ntype: Note\n---\n\nOriginal";
-
-function jsonResponse(body: unknown, status = 200): Response {
-  return new Response(JSON.stringify(body), {
-    status,
-    headers: { "Content-Type": "application/json" },
-  });
-}
-
-test("Edit and Apply send canonical Markdown and publish the applied result", async () => {
-  const requests: Array<{ url: string; init?: RequestInit }> = [];
-  let appliedBody = "";
-  globalThis.fetch = async (input, init) => {
-    requests.push({ url: String(input), init });
-    if (init?.method === "PUT") {
-      return jsonResponse({
-        resource,
-        source: originalSource.replace("Original", "Updated"),
-        body: "Updated",
-        revision: "sha256:updated",
-        editable: true,
-        changed: true,
-      });
-    }
-    return jsonResponse({
-      resource,
-      source: originalSource,
-      body: "Original",
-      revision: "sha256:original",
-      editable: true,
-    });
-  };
-
-  const view = render(
-    <MarkdownContentViewer
-      content="Original"
-      resource={resource}
-      onApplied={(result) => { appliedBody = result.body; }}
-    />,
-  );
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  fireEvent.input(textarea, {
-    target: { value: originalSource.replace("Original", "Updated") },
-  });
-  fireEvent.click(view.getByRole("button", { name: "Apply" }));
-
-  await waitFor(() => assert.equal(appliedBody, "Updated"));
-  assert.deepEqual(requests.map(({ init }) => init?.method ?? "GET"), ["GET", "PUT"]);
-  assert.equal(
-    JSON.parse(String(requests[1].init?.body)).expected_revision,
-    "sha256:original",
-  );
-  assert.equal(
-    view.getByRole("tab", { name: "Preview" }).getAttribute("aria-selected"),
-    "true",
-  );
-});
-
-test("Cancel restores the previous view and never sends a PUT", async () => {
-  const methods: string[] = [];
-  globalThis.fetch = async (_input, init) => {
-    methods.push(init?.method ?? "GET");
-    return jsonResponse({
-      resource,
-      source: originalSource,
-      body: "Original",
-      revision: "sha256:original",
-      editable: true,
-    });
-  };
-
-  const view = render(<MarkdownContentViewer content="Original" resource={resource} />);
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  fireEvent.input(textarea, {
-    target: { value: originalSource.replace("Original", "Draft") },
-  });
-  fireEvent.click(view.getByRole("button", { name: "Cancel" }));
-
-  assert.deepEqual(methods, ["GET"]);
-  assert.equal(view.queryByRole("textbox", { name: "Markdown source" }), null);
-  assert.equal(
-    view.getByRole("tab", { name: "Preview" }).getAttribute("aria-selected"),
-    "true",
-  );
-});
-
-test("validation failures keep the draft visible for correction", async () => {
-  globalThis.fetch = async (_input, init) => {
-    if (init?.method === "PUT") {
-      return jsonResponse({
-        detail: {
-          code: "invalid_markdown_frontmatter",
-          message: "Markdown frontmatter contains invalid YAML.",
-        },
-      }, 422);
-    }
-    return jsonResponse({
-      resource,
-      source: originalSource,
-      body: "Original",
-      revision: "sha256:original",
-      editable: true,
-    });
-  };
-
-  const view = render(<MarkdownContentViewer content="Original" resource={resource} />);
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  const invalidDraft = "---\nid: [\n---\n\nDraft";
-  fireEvent.input(textarea, { target: { value: invalidDraft } });
-  fireEvent.click(view.getByRole("button", { name: "Apply" }));
-
-  const alert = await view.findByRole("alert");
-  assert.match(alert.textContent ?? "", /invalid YAML/);
-  assert.equal(
-    (view.getByRole("textbox", { name: "Markdown source" }) as HTMLTextAreaElement)
-      .value,
-    invalidDraft,
-  );
-});
-
-
-test("resource changes discard the previous editor session", async () => {
-  globalThis.fetch = async (input) => {
-    const id = String(input).endsWith("node-2") ? "node-2" : "node-1";
-    return jsonResponse({
-      resource: { kind: "context-node", id },
-      source: `---\nid: ${id}\ntype: Note\n---\n\n${id}`,
-      body: id,
-      revision: `sha256:${id}`,
-      editable: true,
-    });
-  };
-
-  const view = render(
-    <MarkdownContentViewer content="node-1" resource={resource} />,
-  );
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  fireEvent.input(textarea, {
-    target: { value: `${(textarea as HTMLTextAreaElement).value}\nDraft` },
-  });
-
-  view.rerender(
-    <MarkdownContentViewer
-      content="node-2"
-      resource={{ kind: "context-node", id: "node-2" }}
-    />,
-  );
-  await waitFor(() => assert.equal(
-    view.queryByRole("textbox", { name: "Markdown source" }),
-    null,
-  ));
-
-  view.rerender(
-    <MarkdownContentViewer content="node-1" resource={resource} />,
-  );
-  await waitFor(() => assert.equal(
-    view.queryByRole("textbox", { name: "Markdown source" }),
-    null,
-  ));
-  assert.ok(view.getByRole("button", { name: "Edit" }));
-});
-
-
-test("unmounting a dirty editor clears the parent dirty guard", async () => {
-  const dirtyStates: boolean[] = [];
-  globalThis.fetch = async () => jsonResponse({
-    resource,
-    source: originalSource,
-    body: "Original",
-    revision: "sha256:original",
-    editable: true,
-  });
-
-  const view = render(
-    <MarkdownContentViewer
-      content="Original"
-      resource={resource}
-      onDirtyChange={(dirty) => dirtyStates.push(dirty)}
-    />,
-  );
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  fireEvent.input(textarea, {
-    target: { value: originalSource.replace("Original", "Draft") },
-  });
-  await waitFor(() => assert.equal(dirtyStates.at(-1), true));
-
-  view.unmount();
-
-  assert.equal(dirtyStates.at(-1), false);
-});
-
-test("MemoryWorkspace protects a dirty memory draft when selection changes", async () => {
-  const requestedUrls: string[] = [];
-  globalThis.fetch = async (input) => {
-    const url = String(input);
-    requestedUrls.push(url);
-    if (url.startsWith("/api/memories")) {
-      return jsonResponse({
-        items: [
-          { id: "mem-1", type: "note", excerpt: "First", updated_at: null },
-          { id: "mem-2", type: "note", excerpt: "Second", updated_at: null },
-        ],
-        total: 2,
-        skip: 0,
-        limit: 100,
-      });
-    }
-    const id = url.endsWith("mem-2") ? "mem-2" : "mem-1";
-    return jsonResponse({
-      resource: { kind: "agent-memory", id },
-      source: `---\nid: ${id}\ntype: note\n---\n\n${id}`,
-      body: id,
-      revision: `sha256:${id}`,
-      editable: true,
-    });
-  };
-
-  const view = render(<MemoryWorkspace />);
-  await view.findByText("Selected memory");
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  fireEvent.input(textarea, {
-    target: { value: `${(textarea as HTMLTextAreaElement).value}\nDraft` },
-  });
-
-  dom.window.confirm = () => false;
-  fireEvent.click(view.getByRole("button", { name: /mem-2/ }));
-
-  assert.equal(requestedUrls.some((url) => url.endsWith("mem-2")), false);
-  assert.equal(view.getByText("mem-1", { selector: "strong" }).textContent, "mem-1");
-});
-
-
-test("MemoryWorkspace loads memories beyond the first server page", async () => {
-  const requestedUrls: string[] = [];
-  const firstPage = Array.from({ length: 100 }, (_, index) => ({
-    id: `mem-${index + 1}`,
-    type: "note",
-    excerpt: `Memory ${index + 1}`,
-    updated_at: null,
-  }));
-  globalThis.fetch = async (input) => {
-    const url = String(input);
-    requestedUrls.push(url);
-    if (url === "/api/memories?skip=0&limit=100") {
-      return jsonResponse({
-        items: firstPage,
-        total: 101,
-        skip: 0,
-        limit: 100,
-      });
-    }
-    if (url === "/api/memories?skip=100&limit=100") {
-      return jsonResponse({
-        items: [{
-          id: "mem-101",
-          type: "note",
-          excerpt: "Memory 101",
-          updated_at: null,
-        }],
-        total: 101,
-        skip: 100,
-        limit: 100,
-      });
-    }
-    return jsonResponse({
-      resource: { kind: "agent-memory", id: "mem-1" },
-      source: "---\nid: mem-1\ntype: note\n---\n\nmem-1",
-      body: "mem-1",
-      revision: "sha256:mem-1",
-      editable: true,
-    });
-  };
-
-  const view = render(<MemoryWorkspace />);
-  await view.findByText("Selected memory");
-  fireEvent.click(view.getByRole("button", { name: "Load more memories" }));
-
-  await view.findByRole("button", { name: /mem-101/ });
-  assert.ok(requestedUrls.includes("/api/memories?skip=100&limit=100"));
-  assert.equal(view.getByText("101 of 101 loaded").textContent, "101 of 101 loaded");
-});
-
-
-test("MemoryWorkspace ignores stale selection responses", async () => {
-  let resolveMem2: ((response: Response) => void) | undefined;
-  let resolveMem3: ((response: Response) => void) | undefined;
-  const mem2Response = new Promise<Response>((resolve) => {
-    resolveMem2 = resolve;
-  });
-  const mem3Response = new Promise<Response>((resolve) => {
-    resolveMem3 = resolve;
-  });
-
-  globalThis.fetch = async (input) => {
-    const url = String(input);
-    if (url.startsWith("/api/memories")) {
-      return jsonResponse({
-        items: [
-          { id: "mem-1", type: "note", excerpt: "First", updated_at: null },
-          { id: "mem-2", type: "note", excerpt: "Second", updated_at: null },
-          { id: "mem-3", type: "note", excerpt: "Third", updated_at: null },
-        ],
-        total: 3,
-        skip: 0,
-        limit: 100,
-      });
-    }
-    if (url.endsWith("mem-2")) return mem2Response;
-    if (url.endsWith("mem-3")) return mem3Response;
-    return jsonResponse({
-      resource: { kind: "agent-memory", id: "mem-1" },
-      source: "---\nid: mem-1\ntype: note\n---\n\nmem-1",
-      body: "mem-1",
-      revision: "sha256:mem-1",
-      editable: true,
-    });
-  };
-
-  const view = render(<MemoryWorkspace />);
-  await view.findByText("Selected memory");
-  fireEvent.click(view.getByRole("button", { name: /mem-2/ }));
-  fireEvent.click(view.getByRole("button", { name: /mem-3/ }));
-
-  await act(async () => {
-    resolveMem3?.(jsonResponse({
-      resource: { kind: "agent-memory", id: "mem-3" },
-      source: "---\nid: mem-3\ntype: note\n---\n\nmem-3",
-      body: "mem-3",
-      revision: "sha256:mem-3",
-      editable: true,
-    }));
-    await mem3Response;
-  });
-  await waitFor(() => assert.equal(
-    view.getByText("mem-3", { selector: "strong" }).textContent,
-    "mem-3",
-  ));
-
-  await act(async () => {
-    resolveMem2?.(jsonResponse({
-      resource: { kind: "agent-memory", id: "mem-2" },
-      source: "---\nid: mem-2\ntype: note\n---\n\nmem-2",
-      body: "mem-2",
-      revision: "sha256:mem-2",
-      editable: true,
-    }));
-    await mem2Response;
-  });
-
-  assert.equal(
-    view.getByText("mem-3", { selector: "strong" }).textContent,
-    "mem-3",
-  );
-});
-
-
-test("MemoryWorkspace refreshes frontmatter summaries after apply", async () => {
-  let listRequests = 0;
-  globalThis.fetch = async (input, init) => {
-    const url = String(input);
-    if (url.startsWith("/api/memories")) {
-      listRequests += 1;
-      const saved = listRequests > 1;
-      return jsonResponse({
-        items: [{
-          id: "mem-1",
-          type: saved ? "decision" : "note",
-          excerpt: saved ? "Updated memory" : "Original memory",
-          updated_at: saved ? "2026-09-01T12:00:00+00:00" : null,
-        }],
-        total: 1,
-        skip: 0,
-        limit: 100,
-      });
-    }
-    if (init?.method === "PUT") {
-      return jsonResponse({
-        resource: { kind: "agent-memory", id: "mem-1" },
-        source: "---\nid: mem-1\ntype: decision\n---\n\nUpdated memory",
-        body: "Updated memory",
-        revision: "sha256:updated",
-        editable: true,
-        changed: true,
-      });
-    }
-    return jsonResponse({
-      resource: { kind: "agent-memory", id: "mem-1" },
-      source: "---\nid: mem-1\ntype: note\n---\n\nOriginal memory",
-      body: "Original memory",
-      revision: "sha256:original",
-      editable: true,
-    });
-  };
-
-  const view = render(<MemoryWorkspace />);
-  await view.findByText("Selected memory");
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  fireEvent.input(textarea, {
-    target: {
-      value: (textarea as HTMLTextAreaElement).value
-        .replace("type: note", "type: decision")
-        .replace("Original memory", "Updated memory"),
-    },
-  });
-  fireEvent.click(view.getByRole("button", { name: "Apply" }));
-
-  await view.findByText("decision");
-  assert.equal(listRequests, 2);
-  assert.equal(view.getAllByText("Updated memory").length, 2);
-});
-
-test("HTTP 409 conflict preserves draft and shows conflict error with reload option", async () => {
-  // After a 409, the user's draft must be kept and a recovery path available.
-  const requests: Array<{ method: string; body?: unknown }> = [];
-  let fetchCount = 0;
-
-  globalThis.fetch = async (input, init) => {
-    fetchCount += 1;
-    const method = init?.method ?? "GET";
-    let parsedBody: unknown = undefined;
-    if (init?.body) {
-      try { parsedBody = JSON.parse(String(init.body)); } catch { /* ignore */ }
-    }
-    requests.push({ method, body: parsedBody });
-
-    if (method === "PUT") {
-      // First PUT returns 409 with current_revision
-      return jsonResponse({
-        detail: {
-          code: "markdown_revision_conflict",
-          message: "This item changed after editing began. Reload the latest version before applying.",
-          current_revision: "sha256:newer",
-        },
-      }, 409);
-    }
-    // All GETs return the canonical document
-    return jsonResponse({
-      resource,
-      source: originalSource,
-      body: "Original",
-      revision: "sha256:original",
-      editable: true,
-    });
-  };
-
-  const view = render(<MarkdownContentViewer content="Original" resource={resource} />);
-
-  // Enter edit mode
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-  const draftValue = originalSource.replace("Original", "My draft");
-  fireEvent.input(textarea, { target: { value: draftValue } });
-
-  // Apply → receives 409
-  fireEvent.click(view.getByRole("button", { name: "Apply" }));
-
-  // Conflict error must appear
-  const alert = await view.findByRole("alert");
-  assert.match(
-    alert.textContent ?? "",
-    /changed after editing|Reload/i,
-    "conflict error message must be shown",
-  );
-
-  // Draft must be preserved in the textarea
-  const textareaAfterConflict = view.getByRole("textbox", { name: "Markdown source" }) as HTMLTextAreaElement;
-  assert.equal(textareaAfterConflict.value, draftValue, "draft must be preserved after 409");
-
-  // A reload / recovery action must be available
-  const reloadButton = view.queryByRole("button", { name: /reload latest/i });
-  assert.ok(reloadButton !== null, "a 'Reload latest' recovery button must be shown");
-
-  // Click reload — should re-fetch the latest canonical document
-  await act(async () => {
-    fireEvent.click(reloadButton!);
-  });
-
-  // After reload the editor is re-initialized with the server's canonical source
-  await waitFor(() => {
-    const refreshedTextarea = view.queryByRole("textbox", { name: "Markdown source" });
-    assert.ok(refreshedTextarea !== null, "editor must still be open after reload");
-    assert.equal(
-      (refreshedTextarea as HTMLTextAreaElement).value,
-      originalSource,
-      "editor must show the server canonical source after reload",
-    );
-  });
-
-  // Reload must have triggered exactly one more GET
-  const getCount = requests.filter((r) => r.method === "GET").length;
-  assert.ok(getCount >= 2, "reload must issue a new GET to fetch the latest canonical document");
-});
-
-
-test("successful retry after 422 uses the original revision and persists changes", async () => {
-  // After a 422 (validation failure), the baseRevision must remain valid so that
-  // correcting the draft and re-applying succeeds without re-fetching the document.
-  let putCallCount = 0;
-
-  globalThis.fetch = async (_input, init) => {
-    const method = init?.method ?? "GET";
-    if (method === "PUT") {
-      putCallCount += 1;
-      if (putCallCount === 1) {
-        // First PUT: validation failure — resource is unchanged
-        return jsonResponse({
-          detail: {
-            code: "invalid_markdown_frontmatter",
-            message: "Markdown frontmatter contains invalid YAML.",
-          },
-        }, 422);
-      }
-      // Second PUT: success with the corrected Markdown
-      const body = JSON.parse(String(init?.body ?? "{}")) as { markdown: string };
-      const correctedBody = body.markdown.includes("Corrected") ? "Corrected body" : "body";
-      return jsonResponse({
-        resource,
-        source: originalSource.replace("Original", "Corrected"),
-        body: correctedBody,
-        revision: "sha256:after-retry",
-        editable: true,
-        changed: true,
-      });
-    }
-    return jsonResponse({
-      resource,
-      source: originalSource,
-      body: "Original",
-      revision: "sha256:original",
-      editable: true,
-    });
-  };
-
-  let appliedRevision = "";
-  const view = render(
-    <MarkdownContentViewer
-      content="Original"
-      resource={resource}
-      onApplied={(result) => { appliedRevision = result.revision; }}
-    />,
-  );
-
-  // Enter edit mode
-  fireEvent.click(view.getByRole("button", { name: "Edit" }));
-  const textarea = await view.findByRole("textbox", { name: "Markdown source" });
-
-  // First attempt: create an invalid draft
-  const invalidDraft = "---\nid: [\n---\n\nInvalid body";
-  fireEvent.input(textarea, { target: { value: invalidDraft } });
-  fireEvent.click(view.getByRole("button", { name: "Apply" }));
-
-  // 422 error appears, draft is preserved
-  const alert = await view.findByRole("alert");
-  assert.match(alert.textContent ?? "", /invalid YAML/i);
-  assert.equal(
-    (view.getByRole("textbox", { name: "Markdown source" }) as HTMLTextAreaElement).value,
-    invalidDraft,
-    "invalid draft must be preserved after 422",
-  );
-
-  // Correct the draft
-  const correctedDraft = originalSource.replace("Original", "Corrected");
-  fireEvent.input(view.getByRole("textbox", { name: "Markdown source" }), {
-    target: { value: correctedDraft },
-  });
-
-  // Apply is re-enabled (still dirty)
-  const applyButton = view.getByRole("button", { name: "Apply" });
-  assert.equal(
-    (applyButton as HTMLButtonElement).disabled,
-    false,
-    "Apply must be re-enabled after correcting the draft",
-  );
-
-  // Second attempt: apply corrected draft
-  fireEvent.click(applyButton);
-
-  // Must succeed — server returns new revision
-  await waitFor(() => assert.equal(appliedRevision, "sha256:after-retry"));
-
-  // Editor returns to preview mode after successful save
-  assert.equal(
-    view.getByRole("tab", { name: "Preview" }).getAttribute("aria-selected"),
-    "true",
-    "editor must return to preview after successful retry",
-  );
-
-  // Error is cleared
-  assert.equal(view.queryByRole("alert"), null, "error banner must be cleared after success");
-
-  // Both PUT attempts were made — retry used original revision (no extra GET between attempts)
-  assert.equal(putCallCount, 2, "exactly two PUT requests must be made (failed + successful retry)");
-});
@@ -1,132 +0,0 @@
-import assert from "node:assert/strict";
-import test from "node:test";
-
-import {
-  cancelEdit,
-  createEditSession,
-  createLoadingSession,
-  isDirty,
-  saveFailed,
-  saveStarted,
-  saveSucceeded,
-  shouldConfirmDiscard,
-  updateDraft,
-} from "../src/workspaces/GraphWorkspace/markdownEditorState.ts";
-
-const resource = { kind: "context-node" as const, id: "node-1" };
-
-
-test("enters loading and editing with the canonical source", () => {
-  const loading = createLoadingSession(resource);
-  const editing = createEditSession(resource, {
-    source: "---\nid: node-1\n---\n\nBody",
-    revision: "sha256:one",
-  });
-
-  assert.equal(loading.status, "loading-document");
-  assert.equal(editing.status, "editing");
-  assert.equal(editing.draft, editing.baseSource);
-  assert.equal(isDirty(editing), false);
-});
-
-
-test("draft changes derive dirty state and clear prior errors", () => {
-  const session = createEditSession(resource, {
-    source: "base",
-    revision: "sha256:one",
-  });
-  const failed = saveFailed(session, {
-    kind: "validation",
-    message: "Invalid",
-  });
-  const edited = updateDraft(failed, "draft");
-
-  assert.equal(edited.status, "editing");
-  assert.equal(edited.error, null);
-  assert.equal(isDirty(edited), true);
-  assert.equal(shouldConfirmDiscard(edited), true);
-});
-
-
-test("cancel discards the edit session without saving", () => {
-  const session = updateDraft(
-    createEditSession(resource, { source: "base", revision: "sha256:one" }),
-    "draft",
-  );
-
-  assert.equal(isDirty(session), true);
-  assert.equal(cancelEdit(), null);
-});
-
-
-test("no-op save never enters saving state", () => {
-  const session = createEditSession(resource, {
-    source: "base",
-    revision: "sha256:one",
-  });
-
-  assert.equal(saveStarted(session), session);
-  assert.equal(isDirty(session), false);
-});
-
-
-test("save success replaces the base source and revision", () => {
-  const session = saveStarted(
-    updateDraft(
-      createEditSession(resource, { source: "base", revision: "sha256:one" }),
-      "draft",
-    ),
-  );
-  const saved = saveSucceeded(session, {
-    source: "canonical saved",
-    revision: "sha256:two",
-  });
-
-  assert.equal(saved.status, "viewing");
-  assert.equal(saved.baseSource, "canonical saved");
-  assert.equal(saved.draft, "canonical saved");
-  assert.equal(saved.baseRevision, "sha256:two");
-  assert.equal(isDirty(saved), false);
-});
-
-
-test("validation, conflict, and save failures retain the draft for retry", () => {
-  const draft = updateDraft(
-    createEditSession(resource, { source: "base", revision: "sha256:one" }),
-    "draft",
-  );
-
-  const validation = saveFailed(draft, {
-    kind: "validation",
-    message: "Invalid",
-  });
-  const conflict = saveFailed(draft, {
-    kind: "conflict",
-    message: "Stale",
-    currentRevision: "sha256:two",
-  });
-  const network = saveFailed(draft, {
-    kind: "network",
-    message: "Offline",
-  });
-
-  assert.equal(validation.status, "validation-error");
-  assert.equal(conflict.status, "conflict");
-  assert.equal(network.status, "save-error");
-  assert.equal(validation.draft, "draft");
-  assert.equal(conflict.draft, "draft");
-  assert.equal(network.draft, "draft");
-  assert.equal(saveStarted(network).status, "saving");
-});
-
-
-test("saving sessions do not allow a competing discard confirmation", () => {
-  const saving = saveStarted(
-    updateDraft(
-      createEditSession(resource, { source: "base", revision: "sha256:one" }),
-      "draft",
-    ),
-  );
-
-  assert.equal(shouldConfirmDiscard(saving), false);
-});
@@ -1,91 +0,0 @@
-import assert from "node:assert/strict";
-import test from "node:test";
-
-import {
-  NodeMarkdownRefreshGuard,
-  buildNodeMarkdownAttributeUpdate,
-  readNodeMarkdownAttributeUpdate,
-} from "../src/workspaces/GraphWorkspace/nodeMarkdownSync.ts";
-
-
-test("saved Markdown updates graph content and its visible label", () => {
-  const update = buildNodeMarkdownAttributeUpdate(
-    "issue-1327",
-    "# Issue 1328888\n\nUpdated body",
-    { status: "implemented" },
-  );
-
-  assert.equal(update.content, "# Issue 1328888\n\nUpdated body");
-  assert.equal(update.label, "# Issue 1328888\n\nUpdated body");
-  assert.deepEqual(update.properties, {
-    status: "implemented",
-    content: "# Issue 1328888\n\nUpdated body",
-  });
-});
-
-
-test("empty Markdown falls back to the stable node id label", () => {
-  const update = buildNodeMarkdownAttributeUpdate("issue-1327", "", {});
-
-  assert.equal(update.label, "issue-1327");
-  assert.equal(update.content, "");
-});
-
-
-test("saved frontmatter is refreshed from the canonical graph node", async () => {
-  const update = await readNodeMarkdownAttributeUpdate(
-    "node/1",
-    async (input) => {
-      assert.equal(String(input), "/api/graph/node?node_id=node%2F1");
-      return new Response(JSON.stringify({
-        id: "node/1",
-        type: "Decision",
-        content: "Updated body",
-        properties: {
-          content: "Updated body",
-          status: "accepted",
-          valid_from: "2026-09-01T00:00:00Z",
-        },
-        valid_from: "2026-09-01T00:00:00Z",
-        valid_until: null,
-      }), {
-        status: 200,
-        headers: { "Content-Type": "application/json" },
-      });
-    },
-  );
-  assert.deepEqual(update, {
-    label: "Updated body",
-    content: "Updated body",
-    properties: {
-      content: "Updated body",
-      status: "accepted",
-      valid_from: "2026-09-01T00:00:00Z",
-    },
-    nodeType: "Decision",
-    valid_from: "2026-09-01T00:00:00Z",
-    valid_until: null,
-  });
-});
-
-
-test("realtime updates invalidate an older local-save refresh", () => {
-  const guard = new NodeMarkdownRefreshGuard();
-  const localSaveRefresh = guard.begin("node-1");
-
-  guard.invalidate("node-1");
-
-  assert.equal(guard.isCurrent("node-1", localSaveRefresh), false);
-});
-
-
-test("refresh invalidation is scoped to one node", () => {
-  const guard = new NodeMarkdownRefreshGuard();
-  const firstNodeRefresh = guard.begin("node-1");
-  const secondNodeRefresh = guard.begin("node-2");
-
-  guard.invalidate("node-1");
-
-  assert.equal(guard.isCurrent("node-1", firstNodeRefresh), false);
-  assert.equal(guard.isCurrent("node-2", secondNodeRefresh), true);
-});
@@ -65,11 +65,9 @@ import os
 import re
 import stat
 import tempfile
-import threading
 from collections import deque
 from dataclasses import dataclass, field
 from datetime import date, datetime, timedelta, timezone
-from functools import wraps
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union

@@ -80,12 +78,6 @@ from ..utils.logging import get_logger
 from ..utils.progress_tracker import get_progress_tracker
 from ..utils.types import EntityDict, RelationshipDict
 from ._markdown_filesystem import find_filesystem_link
-from .markdown import (
-    MarkdownIdentityError,
-    MarkdownResourceNotFoundError,
-    MarkdownRevisionConflictError,
-    markdown_document_revision,
-)


 class _UniqueKeySafeLoader(yaml.SafeLoader):
@@ -166,17 +158,6 @@ class MemoryItem:
        )


-def _with_memory_lock(method):
-    """Serialize AgentMemory state mutations and Markdown revision checks."""
-
-    @wraps(method)
-    def locked(self, *args, **kwargs):
-        with self._memory_lock:
-            return method(self, *args, **kwargs)
-
-    return locked
-
-
 class AgentMemory:
    """
    Agent memory manager with RAG integration and Hierarchical Memory.
@@ -216,7 +197,6 @@ class AgentMemory:
        self.logger = get_logger("agent_memory")
        self.config = config or {}
        self.config.update(kwargs)
-        self._memory_lock = threading.RLock()

        self.vector_store = self.config.get("vector_store")
        self.knowledge_graph = self.config.get("knowledge_graph")
@@ -269,7 +249,6 @@ class AgentMemory:

        self.logger.info(f"Saved agent memory to {path}")

-    @_with_memory_lock
    def load(self, path: str) -> None:
        """
        Load memory state from disk.
@@ -319,7 +298,6 @@ class AgentMemory:

        self.logger.info(f"Loaded agent memory from {path}")

-    @_with_memory_lock
    def store(
        self,
        content: str,
@@ -596,7 +574,6 @@ class AgentMemory:
            "relationships": memory_item.relationships,
        }

-    @_with_memory_lock
    def delete_memory(self, memory_id: str, *, skip_vector: bool = False) -> bool:
        """
        Delete memory item.
@@ -648,7 +625,6 @@ class AgentMemory:
        self.logger.debug(f"Deleted memory item: {memory_id}")
        return True

-    @_with_memory_lock
    def vector_ids_for(self, memory_id: str) -> List[str]:
        """Return the vector-store ids owned by a memory item.

@@ -1160,7 +1136,6 @@ class AgentMemory:
        """
        return self.get_memory(memory_id)

-    @_with_memory_lock
    def update(
        self,
        memory_id: str,
@@ -1441,13 +1416,6 @@ class AgentMemory:

        return results

-    @_with_memory_lock
-    def list_snapshot(
-        self, *, limit: int = 100, offset: int = 0
-    ) -> Tuple[List[Dict[str, Any]], int]:
-        """Return one memory page and its total from the same locked state."""
-        return self.list(limit=limit, offset=offset), len(self.memory_items)
-
    def get_by_conversation(
        self, conversation_id: str, limit: int = 100
    ) -> List[Dict[str, Any]]:
@@ -1663,88 +1631,6 @@ class AgentMemory:
                updated += 1
        return updated

-    @_with_memory_lock
-    def export_item_markdown(self, memory_id: str) -> str:
-        """Return one existing memory item as canonical Markdown.
-
-        Args:
-            memory_id: Stable identifier of the memory item to export.
-
-        Returns:
-            Canonical Markdown containing the memory frontmatter and body.
-
-        Raises:
-            MarkdownResourceNotFoundError: If ``memory_id`` does not exist.
-        """
-        memory = self.get(memory_id)
-        if memory is None:
-            raise MarkdownResourceNotFoundError(
-                f"AgentMemory item {memory_id!r} was not found."
-            )
-        return self._memory_to_markdown(memory)
-
-    @_with_memory_lock
-    def apply_item_markdown(
-        self,
-        memory_id: str,
-        document: str,
-        *,
-        expected_revision: Optional[str] = None,
-    ) -> bool:
-        """Validate and atomically replace one existing memory item.
-
-        Args:
-            memory_id: Stable identifier of the memory item to update.
-            document: Canonical Markdown containing the replacement item.
-            expected_revision: Optional revision returned by
-                :meth:`export_item_markdown`. A mismatch rejects stale edits.
-
-        Returns:
-            ``True`` when the item changed, otherwise ``False``.
-
-        Raises:
-            ValueError: If the Markdown or frontmatter is invalid.
-            MarkdownIdentityError: If the frontmatter changes the memory ID.
-            MarkdownResourceNotFoundError: If ``memory_id`` does not exist.
-            MarkdownRevisionConflictError: If ``expected_revision`` is stale.
-            RuntimeError: If the validated item cannot be persisted.
-        """
-        memory = self._markdown_to_memory_dict(document, source=f"memory {memory_id!r}")
-        document_id = memory["memory_id"]
-        if document_id != memory_id:
-            raise MarkdownIdentityError(
-                f"Frontmatter id {document_id!r} does not match resource id "
-                f"{memory_id!r}."
-            )
-        if not self.exists(memory_id):
-            raise MarkdownResourceNotFoundError(
-                f"AgentMemory item {memory_id!r} was not found."
-            )
-        if expected_revision is not None:
-            # _memory_lock is an RLock; this re-entrant call into
-            # export_item_markdown (also @_with_memory_lock) is intentional
-            # and safe because RLock allows the same thread to re-acquire.
-            current_revision = markdown_document_revision(
-                self.export_item_markdown(memory_id)
-            )
-            if current_revision != expected_revision:
-                raise MarkdownRevisionConflictError(current_revision)
-        if self._markdown_record_matches(memory_id, memory):
-            return False
-
-        success = self._replace_memory_item(
-            memory_id,
-            memory["content"],
-            metadata=memory["metadata"],
-            entities=memory["entities"],
-            relationships=memory["relationships"],
-            timestamp=memory["timestamp"],
-            skip_graph=True,
-        )
-        if not success:
-            raise RuntimeError(f"AgentMemory item {memory_id!r} could not be replaced.")
-        return True
-
    # Export/Import
    def export(
        self,
@@ -1793,7 +1679,6 @@ class AgentMemory:
            return self._export_markdown(memories, destination=destination)
        return export_data

-    @_with_memory_lock
    def import_data(
        self, data: Union[str, Path, Dict[str, Any]], format: str = "json"
    ) -> int:
@@ -131,12 +131,6 @@ from ..utils.progress_tracker import get_progress_tracker
 from ..utils.skos import is_skos_hierarchy_edge, validate_skos_hierarchy
 from ._markdown_filesystem import find_filesystem_link
 from .entity_linker import EntityLinker
-from .markdown import (
-    MarkdownIdentityError,
-    MarkdownResourceNotFoundError,
-    MarkdownRevisionConflictError,
-    markdown_document_revision,
-)


 class _UniqueKeySafeLoader(yaml.SafeLoader):
@@ -1173,157 +1167,6 @@ class ContextGraph:
                )
            )

-    def export_node_markdown(self, node_id: str) -> str:
-        """Return one existing node as canonical Markdown.
-
-        Args:
-            node_id: Stable identifier of the node to export.
-
-        Returns:
-            Canonical Markdown containing the node frontmatter and body.
-
-        Raises:
-            MarkdownResourceNotFoundError: If ``node_id`` does not exist.
-        """
-        with self._lock:
-            node = self.nodes.get(node_id)
-            if node is None:
-                raise MarkdownResourceNotFoundError(
-                    f"ContextGraph node {node_id!r} was not found."
-                )
-            return self._node_markdown_source(node)
-
-    def _node_markdown_source(self, node: ContextNode) -> str:
-        frontmatter = {
-            "id": node.node_id,
-            "type": node.node_type,
-            "properties": copy.deepcopy(node.properties),
-            "metadata": copy.deepcopy(node.metadata),
-            "valid_from": node.valid_from,
-            "valid_until": node.valid_until,
-        }
-        return self._render_markdown_document(
-            frontmatter, node.content, f"node {node.node_id!r}"
-        )
-
-    def apply_node_markdown(
-        self,
-        node_id: str,
-        document: str,
-        *,
-        expected_revision: Optional[str] = None,
-    ) -> bool:
-        """Validate and atomically replace one existing node.
-
-        Args:
-            node_id: Stable identifier of the node to update.
-            document: Canonical Markdown containing the replacement node.
-            expected_revision: Optional revision returned by
-                :meth:`export_node_markdown`. A mismatch rejects stale edits.
-
-        Returns:
-            ``True`` when the node changed, otherwise ``False``.
-
-        Raises:
-            ValueError: If the Markdown or frontmatter is invalid.
-            MarkdownIdentityError: If the frontmatter changes the node ID.
-            MarkdownResourceNotFoundError: If ``node_id`` does not exist.
-            MarkdownRevisionConflictError: If ``expected_revision`` is stale.
-        """
-        source = f"node {node_id!r}"
-        frontmatter, body = self._parse_markdown_document(document, source)
-        candidate = self._parse_markdown_node(frontmatter, body, source)
-        if candidate.node_id != node_id:
-            raise MarkdownIdentityError(
-                f"Frontmatter id {candidate.node_id!r} does not match resource id "
-                f"{node_id!r}."
-            )
-
-        with self._lock:
-            existing = self.nodes.get(node_id)
-            if existing is None:
-                raise MarkdownResourceNotFoundError(
-                    f"ContextGraph node {node_id!r} was not found."
-                )
-            if expected_revision is not None:
-                current_revision = markdown_document_revision(
-                    self._node_markdown_source(existing)
-                )
-                if current_revision != expected_revision:
-                    raise MarkdownRevisionConflictError(current_revision)
-            if existing == candidate:
-                return False
-
-            # Decision index rebuilding can still reject YAML-valid property
-            # shapes, so retain every affected structure until commit succeeds.
-            decision_state_before = {}
-            if (
-                existing.node_type.lower() == "decision"
-                or candidate.node_type.lower() == "decision"
-            ):
-                for attribute in (
-                    "_decisions",
-                    "_decision_index",
-                    "_entity_index",
-                    "_temporal_index",
-                ):
-                    if not hasattr(self, attribute):
-                        decision_state_before[attribute] = None
-                    elif attribute in {"_decision_index", "_entity_index"}:
-                        decision_state_before[attribute] = {
-                            key: set(values)
-                            for key, values in getattr(self, attribute).items()
-                        }
-                    elif attribute == "_temporal_index":
-                        decision_state_before[attribute] = list(
-                            getattr(self, attribute)
-                        )
-                    else:
-                        decision_state_before[attribute] = dict(
-                            getattr(self, attribute)
-                        )
-
-            old_type = existing.node_type
-            try:
-                old_bucket = self.node_type_index.get(old_type)
-                if old_bucket is not None:
-                    old_bucket.discard(node_id)
-                    if not old_bucket:
-                        del self.node_type_index[old_type]
-
-                self.nodes[node_id] = candidate
-                self.node_type_index[candidate.node_type].add(node_id)
-                if (
-                    old_type.lower() == "decision"
-                    or candidate.node_type.lower() == "decision"
-                ):
-                    self._sync_decision_from_node(node_id)
-                payload = candidate.to_dict()
-                self._analytics_cache.clear()
-            except Exception:
-                self.nodes[node_id] = existing
-                candidate_bucket = self.node_type_index.get(candidate.node_type)
-                if candidate_bucket is not None:
-                    candidate_bucket.discard(node_id)
-                    if not candidate_bucket:
-                        del self.node_type_index[candidate.node_type]
-                self.node_type_index[old_type].add(node_id)
-                for attribute, state in decision_state_before.items():
-                    if state is None:
-                        if hasattr(self, attribute):
-                            delattr(self, attribute)
-                    else:
-                        restored = (
-                            defaultdict(set, state)
-                            if attribute in {"_decision_index", "_entity_index"}
-                            else state
-                        )
-                        setattr(self, attribute, restored)
-                raise
-
-        self._emit_mutation("UPDATE_NODE", node_id, payload)
-        return True
-
    def save_to_file(
        self, path: Union[str, Path], format: str = "json"
    ) -> None:
@@ -5104,42 +4947,32 @@ class ContextGraph:
    def _sync_decision_from_node(self, node_id: str) -> None:
        """Synchronise a single decision index entry from the node store.

-        Called after ``add_node_attribute`` mutates a decision node and after
-        ``apply_node_markdown`` replaces a node whose old or new type is
-        ``"decision"``, so that ``_decisions`` and the derived indexes stay
-        consistent without requiring a full rebuild of all decisions.
-
-        Temporal index cleanup (``_temporal_index``) runs unconditionally
-        before the node-type guard so that stale entries are removed even when
-        transitioning a decision node to a non-decision type.  Callers are
-        expected to ensure this is only invoked when at least one of the
-        current or previous node types is ``"decision"``; callers that bypass
-        that invariant will have ``node_id`` silently removed from
-        ``_temporal_index`` even if it was never a decision node.
+        Called after ``add_node_attribute`` mutates a decision node so that
+        ``_decisions`` and the derived indexes stay consistent without
+        requiring a full rebuild of all decisions.
        """
        node = self.nodes.get(node_id)
+        if node is None:
+            return
+        if (getattr(node, "node_type", None) or "").lower() != "decision":
+            return
+
        if not hasattr(self, "_decisions"):
            # Indexes don't exist yet — a full rebuild is safer.
            self._rebuild_decision_indexes()
            return

-        # Remove stale index entries before deciding whether the current node
-        # still belongs in the decision indexes.
-        old = self._decisions.pop(node_id, None)
+        # Remove stale index entries for this decision ID.
+        old = self._decisions.get(node_id)
        if old:
            old_cat = old.get("category", "")
-            if old_cat:
+            if old_cat and node_id in self._decision_index.get(old_cat, set()):
                self._decision_index[old_cat].discard(node_id)
            for ent in old.get("entities", []):
                self._entity_index[ent].discard(node_id)
-        self._temporal_index = [
-            (nid, ts) for nid, ts in self._temporal_index if nid != node_id
-        ]
-
-        if node is None:
-            return
-        if (getattr(node, "node_type", None) or "").lower() != "decision":
-            return
+            self._temporal_index = [
+                (nid, ts) for nid, ts in self._temporal_index if nid != node_id
+            ]

        # Rebuild the entry for this node and re-insert index entries.
        meta: Dict[str, Any] = {}
@@ -1,25 +0,0 @@
-"""Shared revision helpers and errors for single-resource Markdown operations."""
-
-import hashlib
-
-
-class MarkdownResourceNotFoundError(KeyError):
-    """Raised when a Markdown operation targets a missing resource."""
-
-
-class MarkdownIdentityError(ValueError):
-    """Raised when frontmatter changes a resource's stable identity."""
-
-
-class MarkdownRevisionConflictError(ValueError):
-    """Raised when a resource changed after an edit session began."""
-
-    def __init__(self, current_revision: str) -> None:
-        super().__init__("Markdown resource revision does not match.")
-        self.current_revision = current_revision
-
-
-def markdown_document_revision(source: str) -> str:
-    """Return the stable revision token for a canonical Markdown document."""
-    digest = hashlib.sha256(source.encode("utf-8")).hexdigest()
-    return f"sha256:{digest}"
@@ -8,19 +8,16 @@ from contextlib import asynccontextmanager
 from pathlib import Path
 from typing import Optional

-from fastapi import Depends, FastAPI, HTTPException, Request
+from fastapi import Depends, FastAPI, HTTPException, Request, WebSocket, WebSocketDisconnect
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import FileResponse, HTMLResponse, JSONResponse
 from fastapi.staticfiles import StaticFiles

 from .. import __version__
-from ..context.agent_memory import AgentMemory
 from ..context.context_graph import ContextGraph
-from .dependencies import anonymous_access_allowed, get_expected_api_key, require_auth
-from .markdown_resources import MarkdownResourceRegistry
-from .runtime import explorer_capabilities, install_mutation_bridge
+from .dependencies import anonymous_access_allowed, get_expected_api_key, is_valid_api_key, require_auth
 from .session import GraphSession
-from .ws import ConnectionManager, install_graph_updates_websocket
+from .ws import ConnectionManager


 def _read_int_env(name: str, default: int) -> int:
@@ -56,23 +53,37 @@ def _read_explorer_settings() -> dict:
    }


+def _install_mutation_bridge(app: FastAPI, session: GraphSession) -> None:
+    if getattr(session.graph, "_mutation_bridge_installed", False):
+        return
+    session.graph._mutation_bridge_installed = True
+    previous_callback = getattr(session.graph, "mutation_callback", None)
+
+    def on_mutation(event_type: str, entity_id: str, payload: dict) -> None:
+        session.handle_graph_mutation(event_type, entity_id, payload)
+        if callable(previous_callback):
+            previous_callback(event_type, entity_id, payload)
+        loop = getattr(app.state, "event_loop", None)
+        manager = getattr(app.state, "ws_manager", None)
+        if loop is None or manager is None or loop.is_closed():
+            return
+        message = {
+            "event_type": event_type,
+            "entity_id": entity_id,
+            "payload": payload,
+        }
+        asyncio.run_coroutine_threadsafe(
+            manager.broadcast("graph_mutation", message),
+            loop,
+        )
+
+    session.graph.mutation_callback = on_mutation
+
+
 def create_app(
    session: Optional[GraphSession] = None,
    provenance_storage_path: Optional[str] = None,
-    agent_memory: Optional[AgentMemory] = None,
 ) -> FastAPI:
-    """Create an Explorer application over live graph and memory objects.
-
-    Args:
-        session: Graph session exposed by the Explorer. A new in-memory graph
-            session is created when omitted.
-        provenance_storage_path: Optional per-app provenance database path.
-        agent_memory: Existing AgentMemory instance to expose in the Memories
-            workspace. The workspace is unavailable when omitted.
-
-    Returns:
-        Configured FastAPI application.
-    """
    settings = _read_explorer_settings()
    prov_path = provenance_storage_path or settings.get("provenance_storage_path")
    if session is None:
@@ -84,7 +95,6 @@ def create_app(
        active_session = session
        if prov_path is not None:
            active_session.set_provenance_storage_path(prov_path)
-    markdown_resources = MarkdownResourceRegistry(active_session.graph, agent_memory)

    @asynccontextmanager
    async def lifespan(app: FastAPI):
@@ -107,9 +117,7 @@ def create_app(
        app.state.event_loop = asyncio.get_running_loop()
        app.state.ws_manager = ConnectionManager()
        app.state.session = active_session
-        app.state.agent_memory = agent_memory
-        app.state.markdown_resources = markdown_resources
-        install_mutation_bridge(app, active_session)
+        _install_mutation_bridge(app, active_session)
        yield

    app = FastAPI(
@@ -131,7 +139,7 @@ def create_app(
        CORSMiddleware,
        allow_origins=settings["allowed_origins"],
        allow_credentials=_allow_credentials,
-        allow_methods=["GET", "POST", "PUT", "DELETE", "OPTIONS"],
+        allow_methods=["GET", "POST", "DELETE", "OPTIONS"],
        allow_headers=["Content-Type", "Authorization", "X-API-Key"],
        max_age=600,
    )
@@ -162,8 +170,6 @@ def create_app(
    from .routes.enrich import router as enrich_router
    from .routes.export_import import router as export_import_router
    from .routes.graph import router as graph_router
-    from .routes.markdown import router as markdown_router
-    from .routes.memories import router as memories_router
    from .routes.ontology import router as ontology_router
    from .routes.provenance import router as provenance_router
    from .routes.sparql import router as sparql_router
@@ -177,15 +183,54 @@ def create_app(
    app.include_router(temporal_router, dependencies=_auth)
    app.include_router(enrich_router, dependencies=_auth)
    app.include_router(export_import_router, dependencies=_auth)
-    app.include_router(markdown_router, dependencies=_auth)
-    app.include_router(memories_router, dependencies=_auth)
    app.include_router(annotations_router, dependencies=_auth)
    app.include_router(sparql_router, dependencies=_auth)
    app.include_router(provenance_router, dependencies=_auth)
    app.include_router(vocabulary_router, dependencies=_auth)
    app.include_router(ontology_router, dependencies=_auth)

-    install_graph_updates_websocket(app, settings["allowed_origins"])
+    _WS_MAX_MESSAGE_BYTES = 64 * 1024  # 64 KB — control messages only
+
+    @app.websocket("/ws/graph-updates")
+    async def websocket_endpoint(websocket: WebSocket):
+        # CORSMiddleware doesn't cover WebSocket handshakes (Starlette's
+        # CORS support only wraps HTTP), so under SEMANTICA_ALLOW_ANONYMOUS
+        # the key check below accepts any origin — loopback binding isn't a
+        # boundary against a browser, since any page the operator has open
+        # can still reach ws://localhost:.../ws/graph-updates directly.
+        # Reject a foreign Origin explicitly here, against the same
+        # allowlist CORSMiddleware already enforces for HTTP
+        # (GHSA-4643-wpgq-w329). Browsers always send Origin on a
+        # cross-origin WebSocket handshake; native/CLI clients omit it
+        # entirely, so a missing Origin is allowed through — the browser is
+        # the only threat this check is closing.
+        origin = websocket.headers.get("origin")
+        allowed_origins = app.state.explorer_settings["allowed_origins"]
+        if origin is not None and origin not in allowed_origins:
+            await websocket.close(code=4403)  # forbidden
+            return
+
+        # Browsers can't set custom headers on a WebSocket handshake, so
+        # accept the key via header (non-browser clients) or query param
+        # (browser clients), same SEMANTICA_API_KEY the REST routes check.
+        candidate = websocket.headers.get("x-api-key") or websocket.query_params.get("api_key")
+        if not is_valid_api_key(candidate):
+            await websocket.close(code=4401)  # unauthorized
+            return
+
+        manager: ConnectionManager = app.state.ws_manager
+        await manager.connect(websocket)
+        await manager.send_personal(websocket, "connection_ack", {"connected": True})
+        try:
+            while True:
+                message = await websocket.receive_text()
+                if len(message) > _WS_MAX_MESSAGE_BYTES:
+                    await websocket.close(code=1009)  # 1009 = message too big
+                    break
+                if message.strip().lower() == "ping":
+                    await manager.send_personal(websocket, "pong", {"ok": True})
+        except WebSocketDisconnect:
+            manager.disconnect(websocket)

    @app.get("/", include_in_schema=False)
    async def root():
@@ -224,7 +269,6 @@ def create_app(
            "name": "Semantica Knowledge Explorer",
            "version": __version__,
            "status": "active",
-            "capabilities": explorer_capabilities(agent_memory),
        }

    static_dir = Path(__file__).resolve().parent.parent / "static"
@@ -14,8 +14,6 @@ from typing import Optional
 from fastapi import Request, HTTPException, Security, status
 from fastapi.security.api_key import APIKeyHeader

-from ..context.agent_memory import AgentMemory
-from .markdown_resources import MarkdownResourceRegistry
 from .session import GraphSession

 _api_key_header = APIKeyHeader(name="X-API-Key", auto_error=False)
@@ -82,25 +80,3 @@ def get_session(request: Request) -> GraphSession:
            detail="GraphSession not initialized."
        )
    return request.app.state.session
-
-
-def get_markdown_resources(request: Request) -> MarkdownResourceRegistry:
-    """Retrieve the Markdown resource registry stored on ``app.state``."""
-    resources = getattr(request.app.state, "markdown_resources", None)
-    if resources is None:
-        raise HTTPException(
-            status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
-            detail="Markdown resources are not initialized.",
-        )
-    return resources
-
-
-def get_agent_memory(request: Request) -> AgentMemory:
-    """Retrieve the optional AgentMemory configured for Explorer."""
-    memory = getattr(request.app.state, "agent_memory", None)
-    if memory is None:
-        raise HTTPException(
-            status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
-            detail="AgentMemory is not configured for this Explorer instance.",
-        )
-    return memory
@@ -1,283 +0,0 @@
-"""Single-resource Markdown access for Explorer."""
-
-from __future__ import annotations
-
-from dataclasses import dataclass
-from enum import Enum
-from typing import Callable, Dict, Optional, Protocol, TypeVar
-
-import yaml
-
-from ..context.agent_memory import AgentMemory
-from ..context.context_graph import ContextGraph
-from ..context.markdown import (
-    MarkdownIdentityError,
-    MarkdownResourceNotFoundError,
-    MarkdownRevisionConflictError,
-    markdown_document_revision,
-)
-
-
-class MarkdownResourceKind(str, Enum):
-    CONTEXT_NODE = "context-node"
-    AGENT_MEMORY = "agent-memory"
-
-
-@dataclass(frozen=True)
-class MarkdownResourceRef:
-    kind: MarkdownResourceKind
-    id: str
-
-
-@dataclass(frozen=True)
-class MarkdownDocument:
-    resource: MarkdownResourceRef
-    source: str
-    body: str
-    revision: str
-
-
-@dataclass(frozen=True)
-class MarkdownApplyResult(MarkdownDocument):
-    changed: bool
-
-
-class MarkdownResourceError(Exception):
-    """Base class for safe, structured Explorer Markdown failures."""
-
-    code = "markdown_resource_error"
-
-    def __init__(
-        self,
-        message: str,
-        *,
-        field: Optional[str] = None,
-        current_revision: Optional[str] = None,
-    ) -> None:
-        super().__init__(message)
-        self.message = message
-        self.field = field
-        self.current_revision = current_revision
-
-
-class MarkdownResourceNotFound(MarkdownResourceError):
-    code = "markdown_resource_not_found"
-
-
-class InvalidMarkdownFrontmatter(MarkdownResourceError):
-    code = "invalid_markdown_frontmatter"
-
-
-class ResourceIdentityMismatch(MarkdownResourceError):
-    code = "resource_identity_mismatch"
-
-
-class MarkdownRevisionConflict(MarkdownResourceError):
-    code = "markdown_revision_conflict"
-
-
-class MarkdownSaveFailed(MarkdownResourceError):
-    code = "markdown_save_failed"
-
-
-class MarkdownAdapter(Protocol):
-    def export(self, resource_id: str) -> str:
-        ...
-
-    def apply(self, resource_id: str, source: str, expected_revision: str) -> bool:
-        ...
-
-
-_Result = TypeVar("_Result")
-
-
-def _translate_domain_errors(operation: Callable[[], _Result]) -> _Result:
-    try:
-        return operation()
-    except MarkdownResourceNotFoundError as exc:
-        raise MarkdownResourceNotFound(str(exc.args[0])) from exc
-    except MarkdownRevisionConflictError as exc:
-        raise MarkdownRevisionConflict(
-            "This item changed after editing began. Reload the latest "
-            "version before applying.",
-            current_revision=exc.current_revision,
-        ) from exc
-    except MarkdownIdentityError as exc:
-        raise ResourceIdentityMismatch(str(exc), field="id") from exc
-    except ValueError as exc:
-        raise InvalidMarkdownFrontmatter(_safe_validation_message(exc)) from exc
-
-
-class ContextGraphNodeMarkdownAdapter:
-    def __init__(self, graph: ContextGraph) -> None:
-        self._graph = graph
-
-    def export(self, resource_id: str) -> str:
-        return _translate_domain_errors(
-            lambda: self._graph.export_node_markdown(resource_id)
-        )
-
-    def apply(self, resource_id: str, source: str, expected_revision: str) -> bool:
-        return _translate_domain_errors(
-            lambda: self._graph.apply_node_markdown(
-                resource_id,
-                source,
-                expected_revision=expected_revision,
-            )
-        )
-
-
-class AgentMemoryItemMarkdownAdapter:
-    def __init__(self, memory: AgentMemory) -> None:
-        self._memory = memory
-
-    def export(self, resource_id: str) -> str:
-        return _translate_domain_errors(
-            lambda: self._memory.export_item_markdown(resource_id)
-        )
-
-    def apply(self, resource_id: str, source: str, expected_revision: str) -> bool:
-        return _translate_domain_errors(
-            lambda: self._memory.apply_item_markdown(
-                resource_id,
-                source,
-                expected_revision=expected_revision,
-            )
-        )
-
-
-def _safe_validation_message(exc: ValueError) -> str:
-    if isinstance(exc.__cause__, yaml.YAMLError):
-        return "Markdown frontmatter contains invalid YAML."
-    return str(exc)
-
-
-def document_revision(source: str) -> str:
-    """Return the stable revision token for canonical Markdown.
-
-    Args:
-        source: Canonical Markdown source.
-
-    Returns:
-        A SHA-256 revision token suitable for optimistic concurrency checks.
-    """
-    return markdown_document_revision(source)
-
-
-def markdown_body(source: str) -> str:
-    """Extract the body from canonical Markdown emitted by a domain model."""
-    lines = source.splitlines(keepends=True)
-    if not lines or lines[0].rstrip("\r\n") != "---":
-        raise MarkdownSaveFailed("The resource produced invalid canonical Markdown.")
-    closing_index = next(
-        (
-            index
-            for index, line in enumerate(lines[1:], start=1)
-            if line.rstrip("\r\n") == "---"
-        ),
-        None,
-    )
-    if closing_index is None:
-        raise MarkdownSaveFailed("The resource produced invalid canonical Markdown.")
-    body = "".join(lines[closing_index + 1 :])
-    if body.startswith("\r\n"):
-        return body[2:]
-    if body.startswith("\n"):
-        return body[1:]
-    return body
-
-
-class MarkdownResourceRegistry:
-    """Route Markdown operations to their owning domain models."""
-
-    def __init__(
-        self,
-        context_graph: ContextGraph,
-        agent_memory: Optional[AgentMemory] = None,
-    ) -> None:
-        self._adapters: Dict[MarkdownResourceKind, MarkdownAdapter] = {
-            MarkdownResourceKind.CONTEXT_NODE: ContextGraphNodeMarkdownAdapter(
-                context_graph
-            )
-        }
-        if agent_memory is not None:
-            self._adapters[
-                MarkdownResourceKind.AGENT_MEMORY
-            ] = AgentMemoryItemMarkdownAdapter(agent_memory)
-
-    def _adapter(self, kind: MarkdownResourceKind) -> MarkdownAdapter:
-        adapter = self._adapters.get(kind)
-        if adapter is None:
-            raise MarkdownResourceNotFound(
-                f"Markdown resource kind {kind.value!r} is not available."
-            )
-        return adapter
-
-    def read(self, ref: MarkdownResourceRef) -> MarkdownDocument:
-        """Read one resource as canonical Markdown.
-
-        Args:
-            ref: Explicit resource kind and stable identifier.
-
-        Returns:
-            The canonical source, body, and current revision.
-
-        Raises:
-            MarkdownResourceError: If the resource is unavailable or invalid.
-        """
-        try:
-            source = self._adapter(ref.kind).export(ref.id)
-        except MarkdownResourceError:
-            raise
-        except Exception as exc:
-            raise MarkdownSaveFailed(
-                "The Markdown resource could not be read."
-            ) from exc
-        return MarkdownDocument(
-            resource=ref,
-            source=source,
-            body=markdown_body(source),
-            revision=document_revision(source),
-        )
-
-    def apply(
-        self,
-        ref: MarkdownResourceRef,
-        markdown: str,
-        expected_revision: str,
-    ) -> MarkdownApplyResult:
-        """Apply validated Markdown to one existing resource.
-
-        Args:
-            ref: Explicit resource kind and stable identifier.
-            markdown: Replacement canonical Markdown.
-            expected_revision: Revision observed when editing began.
-
-        Returns:
-            The saved canonical document and whether it changed.
-
-        Raises:
-            MarkdownResourceError: If validation, identity, persistence, or
-                revision checks fail.
-        """
-        try:
-            changed = self._adapter(ref.kind).apply(
-                ref.id,
-                markdown,
-                expected_revision,
-            )
-        except MarkdownResourceError:
-            raise
-        except Exception as exc:
-            raise MarkdownSaveFailed(
-                "The edit could not be applied. The existing item was not changed."
-            ) from exc
-
-        saved = self.read(ref)
-        return MarkdownApplyResult(
-            resource=saved.resource,
-            source=saved.source,
-            body=saved.body,
-            revision=saved.revision,
-            changed=changed,
-        )
@@ -87,13 +87,6 @@ def _node_response(node: dict) -> NodeResponse:
    return NodeResponse(**node)


-async def _get_node_or_404(node_id: str, session: GraphSession) -> NodeResponse:
-    node = await asyncio.to_thread(session.get_node, node_id)
-    if node is None:
-        raise HTTPException(status_code=404, detail=f"Node '{node_id}' not found")
-    return _node_response(node)
-
-
 def _edge_response(edge: dict) -> EdgeResponse:
    return EdgeResponse(**edge)

@@ -128,20 +121,15 @@ async def list_nodes(
    )


-@router.get("/node", response_model=NodeResponse)
-async def get_node_by_query(
-    node_id: str = Query(..., description="Exact node ID"),
-    session: GraphSession = Depends(get_session),
-):
-    return await _get_node_or_404(node_id, session)
-
-
@router.get("/node/{node_id}", response_model=NodeResponse)
 async def get_node(
    node_id: str,
    session: GraphSession = Depends(get_session),
 ):
-    return await _get_node_or_404(node_id, session)
+    node = await asyncio.to_thread(session.get_node, node_id)
+    if node is None:
+        raise HTTPException(status_code=404, detail=f"Node '{node_id}' not found")
+    return _node_response(node)


@router.get("/node/{node_id}/neighbors", response_model=list[NeighborResponse])
@@ -453,7 +441,7 @@ async def distance_matrix(
                    embeddings = _get_cached_embeddings(session)
                    src_embedding = embeddings.get(src)
                    tgt_embedding = embeddings.get(tgt)
-
+                    
                    if src_embedding is None or tgt_embedding is None:
                        val = None
                    else:
@@ -463,7 +451,7 @@ async def distance_matrix(
                        tgt_vec = np.array(tgt_embedding)
                        sim = np.dot(src_vec, tgt_vec) / (np.linalg.norm(src_vec) * np.linalg.norm(tgt_vec))
                        val = 1.0 - float(sim) if isinstance(sim, (int, float)) else None
-
+                    
                    matrix[i][j] = val
                    matrix[j][i] = val
                elif path_finder is not None:
@@ -1,115 +0,0 @@
-"""Explorer routes for canonical Markdown resources."""
-
-from typing import NoReturn
-
-from fastapi import APIRouter, Depends, HTTPException, status
-
-from ..dependencies import get_markdown_resources
-from ..markdown_resources import (
-    InvalidMarkdownFrontmatter,
-    MarkdownApplyResult,
-    MarkdownDocument,
-    MarkdownResourceError,
-    MarkdownResourceKind,
-    MarkdownResourceNotFound,
-    MarkdownResourceRef,
-    MarkdownResourceRegistry,
-    MarkdownRevisionConflict,
-    ResourceIdentityMismatch,
-)
-from ..schemas import (
-    MarkdownApplyRequest,
-    MarkdownApplyResponse,
-    MarkdownDocumentResponse,
-)
-
-router = APIRouter(prefix="/api/markdown", tags=["markdown"])
-
-
-def _resource_ref(kind: str, resource_id: str) -> MarkdownResourceRef:
-    try:
-        resource_kind = MarkdownResourceKind(kind)
-    except ValueError:
-        _raise_http_error(
-            MarkdownResourceNotFound(
-                f"Markdown resource kind {kind!r} is not available."
-            )
-        )
-    return MarkdownResourceRef(kind=resource_kind, id=resource_id)
-
-
-def _error_detail(error: MarkdownResourceError) -> dict:
-    detail = {"code": error.code, "message": error.message}
-    if error.field is not None:
-        detail["field"] = error.field
-    if error.current_revision is not None:
-        detail["current_revision"] = error.current_revision
-    return detail
-
-
-def _raise_http_error(error: MarkdownResourceError) -> NoReturn:
-    if isinstance(error, MarkdownResourceNotFound):
-        status_code = status.HTTP_404_NOT_FOUND
-    elif isinstance(error, MarkdownRevisionConflict):
-        status_code = status.HTTP_409_CONFLICT
-    elif isinstance(error, (InvalidMarkdownFrontmatter, ResourceIdentityMismatch)):
-        status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
-    else:
-        status_code = status.HTTP_500_INTERNAL_SERVER_ERROR
-    raise HTTPException(status_code=status_code, detail=_error_detail(error)) from error
-
-
-def _document_response(
-    document: MarkdownDocument,
-) -> MarkdownDocumentResponse:
-    return MarkdownDocumentResponse(
-        resource={
-            "kind": document.resource.kind.value,
-            "id": document.resource.id,
-        },
-        source=document.source,
-        body=document.body,
-        revision=document.revision,
-        editable=True,
-    )
-
-
-def _apply_response(result: MarkdownApplyResult) -> MarkdownApplyResponse:
-    document = _document_response(result)
-    return MarkdownApplyResponse(**document.model_dump(), changed=result.changed)
-
-
-@router.get(
-    "/{kind}/{resource_id:path}",
-    response_model=MarkdownDocumentResponse,
-)
-def read_markdown_resource(
-    kind: str,
-    resource_id: str,
-    resources: MarkdownResourceRegistry = Depends(get_markdown_resources),
-) -> MarkdownDocumentResponse:
-    try:
-        return _document_response(resources.read(_resource_ref(kind, resource_id)))
-    except MarkdownResourceError as error:
-        _raise_http_error(error)
-
-
-@router.put(
-    "/{kind}/{resource_id:path}",
-    response_model=MarkdownApplyResponse,
-)
-def apply_markdown_resource(
-    kind: str,
-    resource_id: str,
-    request: MarkdownApplyRequest,
-    resources: MarkdownResourceRegistry = Depends(get_markdown_resources),
-) -> MarkdownApplyResponse:
-    try:
-        result = resources.apply(
-            _resource_ref(kind, resource_id),
-            request.markdown,
-            request.expected_revision,
-        )
-        return _apply_response(result)
-    except MarkdownResourceError as error:
-        _raise_http_error(error)
@@ -1,41 +0,0 @@
-"""Minimal AgentMemory selection surface for Explorer."""
-
-from fastapi import APIRouter, Depends, Query
-
-from ...context.agent_memory import AgentMemory
-from ..dependencies import get_agent_memory
-from ..schemas import MemoryListResponse, MemorySummaryResponse
-
-router = APIRouter(prefix="/api/memories", tags=["memories"])
-
-
-@router.get("", response_model=MemoryListResponse)
-def list_memories(
-    skip: int = Query(default=0, ge=0),
-    limit: int = Query(default=100, ge=1, le=100),
-    memory: AgentMemory = Depends(get_agent_memory),
-) -> MemoryListResponse:
-    records, total = memory.list_snapshot(offset=skip, limit=limit)
-    items = []
-    for record in records:
-        metadata = record.get("metadata") or {}
-        content = record.get("content") or ""
-        excerpt = " ".join(str(content).split())[:160]
-        items.append(
-            MemorySummaryResponse(
-                id=record["memory_id"],
-                type=str(metadata.get("type") or "general"),
-                excerpt=excerpt,
-                updated_at=(
-                    str(metadata["updated_at"])
-                    if metadata.get("updated_at") is not None
-                    else None
-                ),
-            )
-        )
-    return MemoryListResponse(
-        items=items,
-        total=total,
-        skip=skip,
-        limit=limit,
-    )
@@ -1,45 +0,0 @@
-"""Shared runtime assembly for Explorer entry points."""
-
-import asyncio
-from typing import Dict, Optional
-
-from fastapi import FastAPI
-
-from ..context.agent_memory import AgentMemory
-from .session import GraphSession
-
-
-def explorer_capabilities(agent_memory: Optional[AgentMemory]) -> Dict[str, bool]:
-    """Describe optional Explorer features exposed by the current host."""
-    return {"agent_memory": agent_memory is not None}
-
-
-def install_mutation_bridge(app: FastAPI, session: GraphSession) -> None:
-    """Keep Explorer indexes and WebSocket clients in sync with graph writes."""
-    if getattr(app.state, "_semantica_mutation_bridge_session", None) is session:
-        return
-    previous_callback = getattr(session.graph, "mutation_callback", None)
-
-    def on_mutation(event_type: str, entity_id: str, payload: dict) -> None:
-        session.handle_graph_mutation(event_type, entity_id, payload)
-        if callable(previous_callback):
-            previous_callback(event_type, entity_id, payload)
-        loop = getattr(app.state, "event_loop", None)
-        manager = getattr(app.state, "ws_manager", None)
-        if loop is None or manager is None or loop.is_closed():
-            return
-        asyncio.run_coroutine_threadsafe(
-            manager.broadcast(
-                "graph_mutation",
-                {
-                    "event_type": event_type,
-                    "entity_id": entity_id,
-                    "payload": payload,
-                },
-            ),
-            loop,
-        )
-
-    session.graph.mutation_callback = on_mutation
-    app.state._semantica_mutation_bridge = on_mutation
-    app.state._semantica_mutation_bridge_session = session
@@ -428,39 +428,3 @@ class DistanceExportRequest(BaseModel):
    include: List[str] = Field(
        default_factory=lambda: ["source_id", "target_id", "hop_count", "distance_band"],
    )
-
-
-class MarkdownResourceRefResponse(BaseModel):
-    kind: Literal["context-node", "agent-memory"]
-    id: str
-
-
-class MarkdownDocumentResponse(BaseModel):
-    resource: MarkdownResourceRefResponse
-    source: str
-    body: str
-    revision: str
-    editable: bool = True
-
-
-class MarkdownApplyRequest(BaseModel):
-    markdown: str
-    expected_revision: str = Field(..., pattern=r"^sha256:[0-9a-f]{64}$")
-
-
-class MarkdownApplyResponse(MarkdownDocumentResponse):
-    changed: bool
-
-
-class MemorySummaryResponse(BaseModel):
-    id: str
-    type: str
-    excerpt: str
-    updated_at: Optional[str] = None
-
-
-class MemoryListResponse(BaseModel):
-    items: List[MemorySummaryResponse]
-    total: int
-    skip: int
-    limit: int
@@ -9,53 +9,9 @@ import asyncio
 import json
 import threading
 from datetime import datetime, timezone
-from typing import Any, Dict, List, Sequence, Set
+from typing import Any, Dict, Set

-from fastapi import FastAPI, WebSocket, WebSocketDisconnect
-
-from .dependencies import is_valid_api_key
-
-_WS_MAX_MESSAGE_BYTES = 64 * 1024
-
-
-def install_graph_updates_websocket(
-    app: FastAPI,
-    allowed_origins: Sequence[str],
-) -> None:
-    """Install the authenticated graph-mutation WebSocket endpoint."""
-    allowed_origin_set = frozenset(allowed_origins)
-
-    @app.websocket("/ws/graph-updates")
-    async def websocket_endpoint(websocket: WebSocket) -> None:
-        # CORSMiddleware does not cover WebSocket handshakes. Reject foreign
-        # browser origins against the same allowlist used for HTTP CORS.
-        origin = websocket.headers.get("origin")
-        if origin is not None and origin not in allowed_origin_set:
-            await websocket.close(code=4403)
-            return
-
-        # Browser clients pass the API key as a query parameter because the
-        # WebSocket API cannot set custom headers.
-        candidate = websocket.headers.get("x-api-key") or websocket.query_params.get(
-            "api_key"
-        )
-        if not is_valid_api_key(candidate):
-            await websocket.close(code=4401)
-            return
-
-        manager: ConnectionManager = app.state.ws_manager
-        await manager.connect(websocket)
-        await manager.send_personal(websocket, "connection_ack", {"connected": True})
-        try:
-            while True:
-                message = await websocket.receive_text()
-                if len(message) > _WS_MAX_MESSAGE_BYTES:
-                    await websocket.close(code=1009)
-                    break
-                if message.strip().lower() == "ping":
-                    await manager.send_personal(websocket, "pong", {"ok": True})
-        except WebSocketDisconnect:
-            manager.disconnect(websocket)
+from fastapi import WebSocket


 class ConnectionManager:
@@ -107,7 +63,8 @@ class ConnectionManager:
        with self._lock:
            connections = set(self._active_connections)

-        disconnected: List[WebSocket] = []
+    
+        disconnected: list[WebSocket] = []
        for ws in connections:
            try:
                await ws.send_text(message)
@@ -301,10 +301,7 @@ class GraphValidator:
                    code="ORPHAN_NODES",
                    message=f"Found {len(isolates)} orphan nodes (no relationships).",
                    severity=ValidationSeverity.WARNING,
-                    details={
-                        "count": len(isolates),
-                        "ids": sorted(isolates, key=str)[:10],
-                    }  # Limit output deterministically
+                    details={"count": len(isolates), "ids": isolates[:10]} # Limit output
                ))

        except Exception as e:
@@ -35,7 +35,7 @@ Example Usage:
    >>> llm = LiteLLM(model="openai/gpt-4o", api_key="your-key")
    >>> response = llm.generate("Hello, world!")
    >>> # Or use other providers via LiteLLM
-    >>> llm = LiteLLM(model="anthropic/claude-sonnet-5")
+    >>> llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
    >>> response = llm.generate("Hello, world!")
    >>>
    >>> # Anthropic provider
@@ -31,7 +31,7 @@ class LiteLLM:
    Provides unified interface to 100+ LLM providers through LiteLLM library.
    Supports providers like OpenAI, Anthropic, Groq, Azure, Bedrock, Vertex AI, etc.
    
-    Model format: "provider/model-name" (e.g., "openai/gpt-4o", "anthropic/claude-sonnet-5", "groq/llama-3.1-8b-instant")
+    Model format: "provider/model-name" (e.g., "openai/gpt-4o", "anthropic/claude-sonnet-4-20250514", "groq/llama-3.1-8b-instant")
    
    Example:
        >>> from semantica.llms import LiteLLM
@@ -39,7 +39,7 @@ class LiteLLM:
        >>> response = llm.generate("What is AI?")
        >>> 
        >>> # Use with different providers
-        >>> llm = LiteLLM(model="anthropic/claude-sonnet-5")
+        >>> llm = LiteLLM(model="anthropic/claude-sonnet-4-20250514")
        >>> response = llm.generate("Hello!")
    """

@@ -54,7 +54,7 @@ class LiteLLM:

        Args:
            model: Model identifier in format "provider/model-name"
-                   Examples: "openai/gpt-4o", "anthropic/claude-sonnet-5",
+                   Examples: "openai/gpt-4o", "anthropic/claude-sonnet-4-20250514",
                             "groq/llama-3.1-8b-instant", "azure/gpt-4", etc.
            api_key: API key (optional, can use environment variables)
            **kwargs: Additional LiteLLM options (temperature, max_tokens, etc.)
@@ -162,13 +162,6 @@ from .ontology_validator import (
    run_shacl_validation,
    validate_ontology,
 )
-from .quality_gate import (
-    OntologyQualityGate,
-    OntologyQualityReport,
-    QualityIssue,
-    QualitySeverity,
-    ontology_quality_check,
-)
 from .owl_generator import OWLGenerator
 from .property_generator import PropertyGenerator
 from .registry import MethodRegistry, method_registry
@@ -201,11 +194,6 @@ __all__ = [
    "SHACLValidationReport",
    "SHACLViolation",
    "run_shacl_validation",
-    "OntologyQualityGate",
-    "OntologyQualityReport",
-    "QualityIssue",
-    "QualitySeverity",
-    "ontology_quality_check",
    # OWL/RDF generation
    "OWLGenerator",
    # Requirements and competency questions
@@ -9,7 +9,6 @@ from .property_generator import PropertyGenerator
 from .owl_generator import OWLGenerator
 from .ontology_evaluator import OntologyEvaluator
 from .ontology_validator import OntologyValidator
-from .quality_gate import OntologyQualityGate, OntologyQualityReport
 from .llm_generator import LLMOntologyGenerator
 from ..semantic_extract.triplet_extractor import Triplet

@@ -26,9 +25,6 @@ class OntologyEngine:
        self.owl = OWLGenerator(**config)
        self.evaluator = OntologyEvaluator(**config)
        self.validator = OntologyValidator(**config)
-        self.quality_gate = OntologyQualityGate(
-            validator=self.validator, evaluator=self.evaluator
-        )
        self.llm = LLMOntologyGenerator(**config)
        self.store = config.get("store")

@@ -597,15 +593,6 @@ class OntologyEngine:
    def validate(self, ontology: Dict[str, Any], **options):
        return self.validator.validate(ontology, **options)

-    def quality_check(
-        self,
-        ontology: Dict[str, Any],
-        graph_data: Optional[Dict[str, Any]] = None,
-        **options,
-    ) -> OntologyQualityReport:
-        """Run deterministic ontology quality checks suitable for CI."""
-        return self.quality_gate.check(ontology, graph_data=graph_data, **options)
-
    def to_owl(self, ontology: Dict[str, Any], format: str = "turtle", **options):
        return self.owl.generate_owl(ontology, format=format, **options)

@@ -1,855 +0,0 @@
-"""Deterministic quality checks for ontology and KG pipelines."""
-
-import copy
-import math
-from dataclasses import dataclass, field
-from enum import Enum
-from typing import Any, Dict, Iterable, List, Mapping, Optional, Set, Tuple
-
-from ..kg.graph_validator import GraphValidator
-from .ontology_evaluator import OntologyEvaluator
-from .ontology_validator import OntologyValidator
-
-
-class QualitySeverity(str, Enum):
-    """Severity assigned to a quality finding."""
-
-    INFO = "info"
-    WARNING = "warning"
-    ERROR = "error"
-    CRITICAL = "critical"
-
-
-@dataclass
-class QualityIssue:
-    """A single machine-readable ontology quality finding."""
-
-    code: str
-    message: str
-    severity: QualitySeverity
-    element_id: Optional[str] = None
-    element_type: Optional[str] = None
-    details: Dict[str, Any] = field(default_factory=dict)
-
-    def to_dict(self) -> Dict[str, Any]:
-        """Return a JSON-friendly representation of the issue."""
-        return {
-            "code": self.code,
-            "message": self.message,
-            "severity": self.severity.value,
-            "element_id": self.element_id,
-            "element_type": self.element_type,
-            "details": self.details,
-        }
-
-
-@dataclass
-class OntologyQualityReport:
-    """Result returned by :class:`OntologyQualityGate`."""
-
-    passed: bool
-    issues: List[QualityIssue] = field(default_factory=list)
-    stats: Dict[str, int] = field(default_factory=dict)
-    metrics: Dict[str, float] = field(default_factory=dict)
-    thresholds: Dict[str, Optional[float]] = field(default_factory=dict)
-    threshold_failures: List[str] = field(default_factory=list)
-
-    @property
-    def error_count(self) -> int:
-        """Number of error and critical findings."""
-        return sum(
-            issue.severity in (QualitySeverity.ERROR, QualitySeverity.CRITICAL)
-            for issue in self.issues
-        )
-
-    @property
-    def warning_count(self) -> int:
-        """Number of warning findings."""
-        return sum(issue.severity == QualitySeverity.WARNING for issue in self.issues)
-
-    @property
-    def info_count(self) -> int:
-        """Number of informational findings."""
-        return sum(issue.severity == QualitySeverity.INFO for issue in self.issues)
-
-    def to_dict(self) -> Dict[str, Any]:
-        """Return a JSON-friendly representation of the report."""
-        return {
-            "passed": self.passed,
-            "issues": [issue.to_dict() for issue in self.issues],
-            "stats": {
-                **self.stats,
-                "issues": len(self.issues),
-                "errors": self.error_count,
-                "warnings": self.warning_count,
-                "infos": self.info_count,
-            },
-            "metrics": self.metrics,
-            "thresholds": self.thresholds,
-            "threshold_failures": self.threshold_failures,
-        }
-
-
-class OntologyQualityGate:
-    """Run deterministic, CI-friendly ontology quality checks."""
-
-    DEFAULT_THRESHOLDS: Dict[str, Optional[float]] = {
-        "min_coverage": 0.0,
-        "max_errors": 0.0,
-        "max_warnings": None,
-    }
-    _DATA_PROPERTY_TYPES = {"data", "datatype", "data_property", "literal"}
-    _OBJECT_PROPERTY_TYPES = {"object", "object_property", "relationship"}
-    _KNOWN_DATATYPES = {
-        "string",
-        "boolean",
-        "decimal",
-        "float",
-        "double",
-        "integer",
-        "int",
-        "long",
-        "short",
-        "byte",
-        "date",
-        "datetime",
-        "datetimestamp",
-        "time",
-        "duration",
-        "anyuri",
-    }
-    _BUILTIN_CLASSES = {
-        "owl:thing",
-        "rdfs:resource",
-        "http://www.w3.org/2002/07/owl#thing",
-        "http://www.w3.org/2000/01/rdf-schema#resource",
-    }
-
-    def __init__(
-        self,
-        validator: Optional[OntologyValidator] = None,
-        evaluator: Optional[OntologyEvaluator] = None,
-        thresholds: Optional[Mapping[str, Optional[float]]] = None,
-        fail_on_warnings: bool = False,
-    ) -> None:
-        self.validator = validator or OntologyValidator()
-        self.evaluator = evaluator or OntologyEvaluator()
-        self.thresholds = dict(self.DEFAULT_THRESHOLDS)
-        if thresholds:
-            self.thresholds.update(thresholds)
-        self.fail_on_warnings = fail_on_warnings
-
-    def check(
-        self,
-        ontology: Any,
-        graph_data: Optional[Dict[str, Any]] = None,
-        *,
-        thresholds: Optional[Mapping[str, Optional[float]]] = None,
-        fail_on_warnings: Optional[bool] = None,
-        competency_questions: Optional[List[str]] = None,
-    ) -> OntologyQualityReport:
-        """Check an ontology and optionally its instance graph.
-
-        ``graph_data`` is optional because an ontology can be checked before
-        instances are available. When omitted, embedded ``entities`` and
-        ``relationships`` are checked when present.
-        """
-        active_thresholds = dict(self.thresholds)
-        if thresholds:
-            active_thresholds.update(thresholds)
-        min_coverage, max_errors, max_warnings = self._validate_thresholds(
-            active_thresholds
-        )
-        should_fail_on_warnings = (
-            self.fail_on_warnings if fail_on_warnings is None else fail_on_warnings
-        )
-        issues: List[QualityIssue] = []
-
-        if not isinstance(ontology, dict):
-            self._add_issue(
-                issues,
-                "INVALID_ONTOLOGY",
-                "Ontology must be a dictionary.",
-                QualitySeverity.CRITICAL,
-                element_type="ontology",
-            )
-            return self._build_report(
-                issues,
-                classes=0,
-                properties=0,
-                entities=0,
-                relationships=0,
-                metrics={
-                    "coverage": 0.0,
-                    "class_coverage": 0.0,
-                    "property_coverage": 0.0,
-                },
-                thresholds=active_thresholds,
-                min_coverage=min_coverage,
-                max_errors=max_errors,
-                max_warnings=max_warnings,
-                fail_on_warnings=should_fail_on_warnings,
-            )
-
-        validation = self.validator.validate(ontology)
-        for message in getattr(validation, "errors", []) or []:
-            self._add_issue(
-                issues,
-                "VALIDATOR_ERROR",
-                str(message),
-                QualitySeverity.ERROR,
-                element_type="ontology",
-            )
-        for message in getattr(validation, "warnings", []) or []:
-            self._add_issue(
-                issues,
-                "VALIDATOR_WARNING",
-                str(message),
-                QualitySeverity.WARNING,
-                element_type="ontology",
-            )
-
-        classes = self._read_collection(ontology, "classes", issues)
-        properties = self._read_collection(ontology, "properties", issues)
-        class_aliases, class_ids = self._index_elements(
-            classes, "class", "MISSING_CLASS_ID", issues
-        )
-        referenced_classes: Set[str] = set()
-        self._mark_hierarchy(classes, class_aliases, referenced_classes)
-
-        property_with_endpoints = 0
-        for index, prop in enumerate(properties):
-            if not isinstance(prop, dict):
-                self._add_issue(
-                    issues,
-                    "INVALID_PROPERTY",
-                    f"Property at index {index} must be a dictionary.",
-                    QualitySeverity.ERROR,
-                    element_type="property",
-                    details={"index": index},
-                )
-                continue
-
-            prop_id = self._identifier(prop)
-            if prop_id is None:
-                prop_id = f"property[{index}]"
-                self._add_issue(
-                    issues,
-                    "MISSING_PROPERTY_ID",
-                    f"Property at index {index} has no name or URI.",
-                    QualitySeverity.ERROR,
-                    element_type="property",
-                    details={"index": index},
-                )
-
-            raw_prop_type = prop.get("type")
-            prop_type = (
-                str(raw_prop_type).strip().lower() if raw_prop_type is not None else ""
-            )
-            if not prop_type:
-                self._add_issue(
-                    issues,
-                    "MISSING_PROPERTY_TYPE",
-                    f"Property '{prop_id}' has no type.",
-                    QualitySeverity.ERROR,
-                    element_id=prop_id,
-                    element_type="property",
-                )
-            elif (
-                prop_type not in self._DATA_PROPERTY_TYPES | self._OBJECT_PROPERTY_TYPES
-            ):
-                self._add_issue(
-                    issues,
-                    "UNKNOWN_PROPERTY_TYPE",
-                    f"Property '{prop_id}' has unknown type '{prop_type}'.",
-                    QualitySeverity.WARNING,
-                    element_id=prop_id,
-                    element_type="property",
-                )
-
-            domains = self._values(prop, "domain")
-            ranges = self._values(prop, "range")
-            if domains or ranges:
-                property_with_endpoints += 1
-            else:
-                self._add_issue(
-                    issues,
-                    "ORPHAN_PROPERTY",
-                    f"Property '{prop_id}' has no domain or range.",
-                    QualitySeverity.WARNING,
-                    element_id=prop_id,
-                    element_type="property",
-                )
-            if not domains:
-                self._add_issue(
-                    issues,
-                    "MISSING_DOMAIN",
-                    f"Property '{prop_id}' has no domain.",
-                    QualitySeverity.WARNING,
-                    element_id=prop_id,
-                    element_type="property",
-                )
-            for domain in domains:
-                matched = self._match_class(domain, class_aliases)
-                if matched:
-                    referenced_classes.add(matched)
-                elif not self._is_builtin_class(domain):
-                    self._add_issue(
-                        issues,
-                        "UNKNOWN_DOMAIN",
-                        f"Property '{prop_id}' references unknown domain '{domain}'.",
-                        QualitySeverity.ERROR,
-                        element_id=prop_id,
-                        element_type="property",
-                        details={"domain": domain},
-                    )
-
-            if not ranges:
-                self._add_issue(
-                    issues,
-                    "MISSING_RANGE",
-                    f"Property '{prop_id}' has no range.",
-                    QualitySeverity.WARNING,
-                    element_id=prop_id,
-                    element_type="property",
-                )
-            for range_value in ranges:
-                matched = self._match_class(range_value, class_aliases)
-                if matched:
-                    referenced_classes.add(matched)
-                self._check_range(
-                    prop_id,
-                    prop_type,
-                    range_value,
-                    matched is not None,
-                    issues,
-                )
-
-        graph = graph_data
-        if graph is None and ("entities" in ontology or "relationships" in ontology):
-            graph = ontology
-        graph_entities, graph_relationships = self._read_graph(graph, issues)
-        if self._has_valid_graph_shape(graph):
-            self._check_graph(graph, issues)
-            self._mark_graph_types(graph_entities, class_aliases, referenced_classes)
-
-        for class_id in class_ids:
-            if class_id not in referenced_classes:
-                self._add_issue(
-                    issues,
-                    "ORPHAN_CLASS",
-                    f"Class '{class_id}' is not connected to a property, hierarchy, or graph entity type.",
-                    QualitySeverity.WARNING,
-                    element_id=class_id,
-                    element_type="class",
-                )
-
-        class_coverage = (
-            len(referenced_classes & set(class_ids)) / len(class_ids)
-            if class_ids
-            else 0.0
-        )
-        property_coverage = (
-            property_with_endpoints / len(properties) if properties else 1.0
-        )
-        metrics: Dict[str, float] = {
-            "coverage": (
-                (class_coverage + property_coverage) / 2
-                if classes or properties
-                else 0.0
-            ),
-            "class_coverage": class_coverage,
-            "property_coverage": property_coverage,
-            "validator_valid": 1.0 if getattr(validation, "valid", True) else 0.0,
-        }
-        if competency_questions is not None:
-            evaluation_ontology = self._prepare_for_evaluation(
-                ontology, classes, properties
-            )
-            evaluation = self._evaluate_competency_questions(
-                evaluation_ontology, competency_questions=competency_questions
-            )
-            metrics["competency_question_coverage"] = evaluation.coverage_score
-            metrics["completeness"] = evaluation.completeness_score
-
-        return self._build_report(
-            issues,
-            classes=len(classes),
-            properties=len(properties),
-            entities=len(graph_entities),
-            relationships=len(graph_relationships),
-            metrics=metrics,
-            thresholds=active_thresholds,
-            min_coverage=min_coverage,
-            max_errors=max_errors,
-            max_warnings=max_warnings,
-            fail_on_warnings=should_fail_on_warnings,
-        )
-
-    def _check_range(
-        self,
-        prop_id: str,
-        prop_type: str,
-        range_value: Any,
-        is_class: bool,
-        issues: List[QualityIssue],
-    ) -> None:
-        if prop_type in self._DATA_PROPERTY_TYPES:
-            if not self._is_known_datatype(range_value):
-                self._add_issue(
-                    issues,
-                    "INVALID_DATATYPE_RANGE",
-                    f"Data property '{prop_id}' has invalid range '{range_value}'.",
-                    QualitySeverity.ERROR,
-                    element_id=prop_id,
-                    element_type="property",
-                    details={"range": range_value},
-                )
-        elif prop_type in self._OBJECT_PROPERTY_TYPES:
-            if not is_class and not self._is_builtin_class(range_value):
-                self._add_issue(
-                    issues,
-                    "UNKNOWN_RANGE",
-                    f"Object property '{prop_id}' references unknown range '{range_value}'.",
-                    QualitySeverity.ERROR,
-                    element_id=prop_id,
-                    element_type="property",
-                    details={"range": range_value},
-                )
-        elif (
-            not is_class
-            and not self._is_builtin_class(range_value)
-            and not self._is_known_datatype(range_value)
-        ):
-            self._add_issue(
-                issues,
-                "UNKNOWN_RANGE",
-                f"Property '{prop_id}' references unknown range '{range_value}'.",
-                QualitySeverity.ERROR,
-                element_id=prop_id,
-                element_type="property",
-                details={"range": range_value},
-            )
-
-    def _build_report(
-        self,
-        issues: List[QualityIssue],
-        *,
-        classes: int,
-        properties: int,
-        entities: int,
-        relationships: int,
-        metrics: Dict[str, float],
-        thresholds: Dict[str, Optional[float]],
-        min_coverage: float,
-        max_errors: float,
-        max_warnings: Optional[float],
-        fail_on_warnings: bool,
-    ) -> OntologyQualityReport:
-        failures: List[str] = []
-        error_count = sum(
-            issue.severity in (QualitySeverity.ERROR, QualitySeverity.CRITICAL)
-            for issue in issues
-        )
-        warning_count = sum(
-            issue.severity == QualitySeverity.WARNING for issue in issues
-        )
-        if error_count > max_errors:
-            failures.append("max_errors")
-        if max_warnings is not None and warning_count > max_warnings:
-            failures.append("max_warnings")
-        if fail_on_warnings and warning_count:
-            failures.append("fail_on_warnings")
-        if metrics.get("coverage", 0.0) < min_coverage:
-            failures.append("min_coverage")
-        return OntologyQualityReport(
-            passed=not failures,
-            issues=issues,
-            stats={
-                "classes": classes,
-                "properties": properties,
-                "entities": entities,
-                "relationships": relationships,
-            },
-            metrics=metrics,
-            thresholds=thresholds,
-            threshold_failures=failures,
-        )
-
-    @staticmethod
-    def _validate_thresholds(
-        thresholds: Mapping[str, Optional[float]],
-    ) -> Tuple[float, float, Optional[float]]:
-        min_coverage = float(thresholds.get("min_coverage", 0.0) or 0.0)
-        max_errors = float(thresholds.get("max_errors", 0.0) or 0.0)
-        warning_value = thresholds.get("max_warnings")
-        max_warnings = None if warning_value is None else float(warning_value)
-        if not all(
-            math.isfinite(value)
-            for value in (min_coverage, max_errors)
-            if value is not None
-        ) or (max_warnings is not None and not math.isfinite(max_warnings)):
-            raise ValueError("quality thresholds must be finite numbers")
-        if not 0.0 <= min_coverage <= 1.0:
-            raise ValueError("min_coverage must be between 0.0 and 1.0")
-        if max_errors < 0 or (max_warnings is not None and max_warnings < 0):
-            raise ValueError("error and warning thresholds cannot be negative")
-        return min_coverage, max_errors, max_warnings
-
-    @classmethod
-    def _prepare_for_evaluation(
-        cls,
-        ontology: Dict[str, Any],
-        classes: Iterable[Any],
-        properties: Iterable[Any],
-    ) -> Dict[str, Any]:
-        """Make a shallow, evaluator-safe view without changing caller data."""
-        prepared = dict(ontology)
-        prepared["classes"] = [
-            cls._prepare_element(element)
-            for element in classes
-            if isinstance(element, dict)
-        ]
-        prepared["properties"] = [
-            cls._prepare_element(element)
-            for element in properties
-            if isinstance(element, dict)
-        ]
-        return prepared
-
-    @classmethod
-    def _prepare_element(cls, element: Dict[str, Any]) -> Dict[str, Any]:
-        prepared = dict(element)
-        identifier = cls._identifier(prepared)
-        if identifier is not None and not str(prepared.get("name", "")).strip():
-            prepared["name"] = identifier
-        return prepared
-
-    def _evaluate_competency_questions(
-        self, ontology: Dict[str, Any], competency_questions: List[str]
-    ) -> Any:
-        """Evaluate with an isolated question manager for repeatable checks."""
-        evaluator = copy.copy(self.evaluator)
-        manager = getattr(self.evaluator, "competency_questions_manager", None)
-        if manager is not None and hasattr(manager, "questions"):
-            isolated_manager = copy.copy(manager)
-            isolated_manager.questions = []
-            evaluator.competency_questions_manager = isolated_manager
-        return evaluator.evaluate_ontology(
-            ontology, competency_questions=competency_questions
-        )
-
-    @classmethod
-    def _read_collection(
-        cls, ontology: Dict[str, Any], key: str, issues: List[QualityIssue]
-    ) -> List[Any]:
-        if key not in ontology:
-            cls._add_issue(
-                issues,
-                f"MISSING_{key.upper()}",
-                f"Ontology has no {key} defined.",
-                QualitySeverity.WARNING,
-                element_type="ontology",
-            )
-            return []
-        value = ontology[key]
-        if not isinstance(value, list):
-            cls._add_issue(
-                issues,
-                f"INVALID_{key.upper()}",
-                f"Ontology '{key}' must be a list.",
-                QualitySeverity.ERROR,
-                element_type="ontology",
-            )
-            return []
-        return value
-
-    @classmethod
-    def _index_elements(
-        cls,
-        elements: Iterable[Any],
-        element_type: str,
-        missing_code: str,
-        issues: List[QualityIssue],
-    ) -> Tuple[Dict[str, str], List[str]]:
-        aliases: Dict[str, str] = {}
-        identifiers: List[str] = []
-        for index, element in enumerate(elements):
-            identifier = cls._identifier(element)
-            if identifier is None:
-                cls._add_issue(
-                    issues,
-                    missing_code,
-                    f"{element_type.title()} at index {index} has no name or URI.",
-                    QualitySeverity.ERROR,
-                    element_type=element_type,
-                    details={"index": index},
-                )
-                continue
-            identifiers.append(identifier)
-            aliases_for_element: Set[str] = set()
-            for candidate in cls._identifiers(element):
-                aliases_for_element.update(cls._term_aliases(candidate))
-            for alias in sorted(aliases_for_element):
-                aliases.setdefault(alias, identifier)
-        return aliases, identifiers
-
-    @classmethod
-    def _mark_hierarchy(
-        cls,
-        classes: Iterable[Any],
-        aliases: Mapping[str, str],
-        referenced: Set[str],
-    ) -> None:
-        for class_entry in classes:
-            if not isinstance(class_entry, dict):
-                continue
-            identifier = cls._identifier(class_entry)
-            for key in (
-                "subClassOf",
-                "subclassOf",
-                "parent",
-                "superclass",
-                "superclasses",
-            ):
-                parents = cls._values(class_entry, key)
-                if parents and identifier:
-                    referenced.add(identifier)
-                for parent in parents:
-                    matched = cls._match_class(parent, aliases)
-                    if matched:
-                        referenced.add(matched)
-
-    @classmethod
-    def _mark_graph_types(
-        cls,
-        entities: Iterable[Any],
-        aliases: Mapping[str, str],
-        referenced: Set[str],
-    ) -> None:
-        for entity in entities:
-            if not isinstance(entity, dict):
-                continue
-            entity_type = entity.get("type") or entity.get("entity_type")
-            matched = cls._match_class(entity_type, aliases)
-            if matched:
-                referenced.add(matched)
-
-    @classmethod
-    def _check_graph(cls, graph: Dict[str, Any], issues: List[QualityIssue]) -> None:
-        safe_graph = cls._prepare_graph_for_validation(graph, issues)
-        result = GraphValidator().validate(safe_graph)
-        code_map = {
-            "DANGLING_EDGE": "UNRESOLVED_RELATIONSHIP_ENDPOINT",
-            "ORPHAN_NODES": "ORPHAN_ENTITY",
-        }
-        severity_map = {
-            "info": QualitySeverity.INFO,
-            "warning": QualitySeverity.WARNING,
-            "error": QualitySeverity.ERROR,
-            "critical": QualitySeverity.CRITICAL,
-        }
-        for graph_issue in result.issues:
-            severity = severity_map.get(
-                graph_issue.severity.value, QualitySeverity.ERROR
-            )
-            details = dict(graph_issue.details or {})
-            if graph_issue.code == "ORPHAN_NODES" and "ids" in details:
-                details["ids"] = sorted(details["ids"], key=str)
-            cls._add_issue(
-                issues,
-                code_map.get(graph_issue.code, graph_issue.code),
-                graph_issue.message,
-                severity,
-                element_id=graph_issue.element_id,
-                element_type=graph_issue.element_type,
-                details=details,
-            )
-
-    @classmethod
-    def _prepare_graph_for_validation(
-        cls, graph: Dict[str, Any], issues: List[QualityIssue]
-    ) -> Dict[str, List[Dict[str, Any]]]:
-        """Normalize supported graph aliases and isolate malformed members."""
-        entities: List[Dict[str, Any]] = []
-        raw_entities = graph.get("entities", [])
-        raw_relationships = graph.get("relationships", [])
-        for index, entity in enumerate(
-            raw_entities if isinstance(raw_entities, list) else []
-        ):
-            if not isinstance(entity, dict):
-                cls._add_issue(
-                    issues,
-                    "INVALID_ENTITY",
-                    f"Entity at index {index} must be a dictionary.",
-                    QualitySeverity.ERROR,
-                    element_type="entity",
-                    details={"index": index},
-                )
-                continue
-            normalized = dict(entity)
-            if not normalized.get("name") and normalized.get("text") is not None:
-                normalized["name"] = normalized["text"]
-            entities.append(normalized)
-
-        relationships: List[Dict[str, Any]] = []
-        for index, relationship in enumerate(
-            raw_relationships if isinstance(raw_relationships, list) else []
-        ):
-            if not isinstance(relationship, dict):
-                cls._add_issue(
-                    issues,
-                    "INVALID_RELATIONSHIP",
-                    f"Relationship at index {index} must be a dictionary.",
-                    QualitySeverity.ERROR,
-                    element_type="relationship",
-                    details={"index": index},
-                )
-                continue
-            relationships.append(dict(relationship))
-
-        return {"entities": entities, "relationships": relationships}
-
-    @classmethod
-    def _read_graph(
-        cls, graph: Optional[Dict[str, Any]], issues: List[QualityIssue]
-    ) -> Tuple[List[Any], List[Any]]:
-        if graph is None:
-            return [], []
-        if not isinstance(graph, dict):
-            cls._add_issue(
-                issues,
-                "INVALID_GRAPH",
-                "Graph data must be a dictionary.",
-                QualitySeverity.ERROR,
-                element_type="graph",
-            )
-            return [], []
-        entities = graph.get("entities", [])
-        relationships = graph.get("relationships", [])
-        if not isinstance(entities, list) or not isinstance(relationships, list):
-            cls._add_issue(
-                issues,
-                "INVALID_GRAPH",
-                "Graph entities and relationships must be lists.",
-                QualitySeverity.ERROR,
-                element_type="graph",
-            )
-            return [], []
-        return entities, relationships
-
-    @staticmethod
-    def _has_valid_graph_shape(graph: Optional[Dict[str, Any]]) -> bool:
-        return bool(
-            isinstance(graph, dict)
-            and isinstance(graph.get("entities", []), list)
-            and isinstance(graph.get("relationships", []), list)
-        )
-
-    @staticmethod
-    def _identifier(element: Any) -> Optional[str]:
-        identifiers = OntologyQualityGate._identifiers(element)
-        return identifiers[0] if identifiers else None
-
-    @staticmethod
-    def _identifiers(element: Any) -> List[str]:
-        if isinstance(element, dict):
-            values = []
-            for key in ("name", "uri", "id", "@id"):
-                value = element.get(key)
-                if value is not None and str(value).strip():
-                    values.append(str(value).strip())
-            return values
-        if isinstance(element, str) and element.strip():
-            return [element.strip()]
-        return []
-
-    @staticmethod
-    def _values(element: Dict[str, Any], key: str) -> List[Any]:
-        value = element.get(key)
-        if value is None:
-            return []
-        if isinstance(value, (list, tuple, set)):
-            values = [item for item in value if item is not None and str(item).strip()]
-            return sorted(values, key=str) if isinstance(value, set) else values
-        return [value] if str(value).strip() else []
-
-    @classmethod
-    def _term_aliases(cls, value: Any) -> Set[str]:
-        if isinstance(value, dict):
-            value = cls._identifier(value)
-        if value is None:
-            return set()
-        text = str(value).strip().strip("<>")
-        if not text:
-            return set()
-        aliases = {text, text.lower()}
-        for separator in ("#", "/"):
-            if separator in text:
-                local = text.rstrip("/").rsplit(separator, 1)[-1]
-                aliases.update({local, local.lower()})
-        if ":" in text and not text.startswith(("http://", "https://")):
-            local = text.rsplit(":", 1)[-1]
-            aliases.update({local, local.lower()})
-        return aliases
-
-    @classmethod
-    def _match_class(cls, value: Any, aliases: Mapping[str, str]) -> Optional[str]:
-        for alias in sorted(cls._term_aliases(value)):
-            if alias in aliases:
-                return aliases[alias]
-        return None
-
-    @classmethod
-    def _is_builtin_class(cls, value: Any) -> bool:
-        return any(alias in cls._BUILTIN_CLASSES for alias in cls._term_aliases(value))
-
-    @classmethod
-    def _is_known_datatype(cls, value: Any) -> bool:
-        return any(alias in cls._KNOWN_DATATYPES for alias in cls._term_aliases(value))
-
-    @staticmethod
-    def _add_issue(
-        issues: List[QualityIssue],
-        code: str,
-        message: str,
-        severity: QualitySeverity,
-        *,
-        element_id: Optional[str] = None,
-        element_type: Optional[str] = None,
-        details: Optional[Dict[str, Any]] = None,
-    ) -> None:
-        issues.append(
-            QualityIssue(
-                code=code,
-                message=message,
-                severity=severity,
-                element_id=element_id,
-                element_type=element_type,
-                details=details or {},
-            )
-        )
-
-
-def ontology_quality_check(
-    ontology: Any,
-    graph_data: Optional[Dict[str, Any]] = None,
-    *,
-    thresholds: Optional[Mapping[str, Optional[float]]] = None,
-    fail_on_warnings: bool = False,
-    competency_questions: Optional[List[str]] = None,
-    validator: Optional[OntologyValidator] = None,
-    evaluator: Optional[OntologyEvaluator] = None,
-) -> OntologyQualityReport:
-    """Convenience wrapper around :class:`OntologyQualityGate`."""
-    gate = OntologyQualityGate(
-        validator=validator,
-        evaluator=evaluator,
-        thresholds=thresholds,
-        fail_on_warnings=fail_on_warnings,
-    )
-    return gate.check(
-        ontology,
-        graph_data=graph_data,
-        competency_questions=competency_questions,
-    )
@@ -5,7 +5,6 @@ This module provides the REST API server for the Semantica framework
 using FastAPI and uvicorn.
 """

-import asyncio
 import logging
 import os
 import uvicorn
@@ -25,10 +24,8 @@ from .utils.logging import setup_logging
 try:
    from .context.context_graph import ContextGraph
    from .explorer.session import GraphSession
-    from .explorer.ws import ConnectionManager, install_graph_updates_websocket
+    from .explorer.ws import ConnectionManager
    from .explorer.dependencies import anonymous_access_allowed, get_expected_api_key, require_auth
-    from .explorer.markdown_resources import MarkdownResourceRegistry
-    from .explorer.runtime import explorer_capabilities, install_mutation_bridge
    EXPLORER_AVAILABLE = True
 except ImportError:
    EXPLORER_AVAILABLE = False
@@ -60,24 +57,16 @@ async def lifespan(app: FastAPI):
            graph = ContextGraph()
            app.state.session = GraphSession(graph)
            app.state.ws_manager = ConnectionManager()
-            app.state.event_loop = asyncio.get_running_loop()
-            app.state.agent_memory = None
-            app.state.markdown_resources = MarkdownResourceRegistry(graph)
-            install_mutation_bridge(app, app.state.session)
            logging.info("Database Session and WebSockets attached to app state.")
        except Exception as e:
            logging.error(f"Failed to initialize GraphSession: {e}")
            app.state.session = None
            app.state.ws_manager = None
-            app.state.agent_memory = None
-            app.state.markdown_resources = None
    else:
        app.state.session = None
        app.state.ws_manager = None
-        app.state.agent_memory = None
-        app.state.markdown_resources = None

-    yield
+    yield  

    logging.info("Shutting down Semantica API...")
    if getattr(app.state, "session", None) and hasattr(app.state.session.graph, "close"):
@@ -102,14 +91,11 @@ app.add_middleware(
    CORSMiddleware,
    allow_origins=_cors_origins,
    allow_credentials=True,
-    allow_methods=["GET", "POST", "PUT", "DELETE", "OPTIONS"],
+    allow_methods=["GET", "POST", "DELETE", "OPTIONS"],
    allow_headers=["Content-Type", "Authorization", "X-API-Key"],
    max_age=600,
 )

-if EXPLORER_AVAILABLE:
-    install_graph_updates_websocket(app, _cors_origins)
-

 # --- Security response headers -------------------------------------
 class _SecurityHeadersMiddleware(BaseHTTPMiddleware):
@@ -152,10 +138,7 @@ async def root():
    return {
        "name": "Semantica API",
        "version": __version__,
-        "status": "active",
-        "capabilities": explorer_capabilities(
-            getattr(app.state, "agent_memory", None)
-        ),
+        "status": "active"
    }

@app.get("/health")
@@ -182,8 +165,6 @@ if EXPLORER_AVAILABLE:
            enrich,
            export_import,
            graph,
-            markdown,
-            memories,
            ontology,
            temporal,
            vocabulary,
@@ -198,8 +179,6 @@ if EXPLORER_AVAILABLE:
        app.include_router(enrich.router, dependencies=_auth)
        app.include_router(export_import.router, dependencies=_auth)
        app.include_router(graph.router, dependencies=_auth)
-        app.include_router(markdown.router, dependencies=_auth)
-        app.include_router(memories.router, dependencies=_auth)
        app.include_router(ontology.router, dependencies=_auth)
        app.include_router(temporal.router, dependencies=_auth)
        app.include_router(vocabulary.router, dependencies=_auth)
@@ -281,4 +260,4 @@ def main():
    uvicorn.run(app, host=host, port=8000)

 if __name__ == "__main__":
-    main()
+    main()
@@ -12,10 +12,6 @@ import pytest
 import yaml

 from semantica.context.agent_memory import AgentMemory
-from semantica.context.markdown import (
-    MarkdownRevisionConflictError,
-    markdown_document_revision,
-)

 _ERROR_PRIVILEGE_NOT_HELD = 1314

@@ -1012,144 +1008,3 @@ def test_markdown_import_rejects_non_regular_file(tmp_path):
    with patch("semantica.context.agent_memory.os.fstat", return_value=fake_stat):
        with pytest.raises(ValueError, match="not a regular file"):
            memory._read_markdown_file_content(real_file)
-
-
-def _editable_memory(vector_store=None):
-    memory = AgentMemory(vector_store=vector_store)
-    memory.store(
-        "Original body",
-        memory_id="mem-edit",
-        timestamp=datetime.fromisoformat("2026-07-22T09:00:00+00:00"),
-        metadata={
-            "type": "note",
-            "updated_at": "2026-07-22T10:00:00+00:00",
-            "owner": "before",
-        },
-    )
-    return memory
-
-
-def test_single_item_markdown_export_and_apply_preserve_identity():
-    memory = _editable_memory()
-    source = memory.export_item_markdown("mem-edit")
-    edited = source.replace("owner: before", "owner: after").replace(
-        "Original body", "Updated body"
-    )
-
-    assert memory.apply_item_markdown("mem-edit", edited) is True
-    item = memory.get("mem-edit")
-    assert item["memory_id"] == "mem-edit"
-    assert item["content"] == "Updated body"
-    assert item["metadata"]["owner"] == "after"
-    assert memory.export_item_markdown("mem-edit") == edited
-
-
-def test_single_item_markdown_rejects_identity_change_without_mutation():
-    memory = _editable_memory()
-    before = deepcopy(memory.get("mem-edit"))
-    document = memory.export_item_markdown("mem-edit").replace(
-        "id: mem-edit", "id: mem-other"
-    )
-
-    with pytest.raises(ValueError, match="does not match resource id"):
-        memory.apply_item_markdown("mem-edit", document)
-
-    assert memory.get("mem-edit") == before
-    assert memory.get("mem-other") is None
-
-
-def test_single_item_markdown_invalid_document_and_missing_item_are_safe():
-    memory = _editable_memory()
-    before = deepcopy(memory.get("mem-edit"))
-
-    with pytest.raises(ValueError, match="Invalid Markdown frontmatter"):
-        memory.apply_item_markdown("mem-edit", "---\nid: [\n---\n\nBroken")
-    with pytest.raises(KeyError, match="missing"):
-        memory.export_item_markdown("missing")
-
-    assert memory.get("mem-edit") == before
-
-
-def test_single_item_markdown_noop_skips_vector_sync():
-    vector_store = TrackingVectorStore()
-    memory = _editable_memory(vector_store=vector_store)
-    vector_store.events.clear()
-    source = memory.export_item_markdown("mem-edit")
-
-    assert memory.apply_item_markdown("mem-edit", source) is False
-    assert vector_store.events == []
-
-
-def test_single_item_markdown_revision_check_is_atomic_with_apply():
-    memory = _editable_memory()
-    source = memory.export_item_markdown("mem-edit")
-    expected_revision = markdown_document_revision(source)
-    memory.update("mem-edit", content="Concurrent update")
-
-    with pytest.raises(MarkdownRevisionConflictError):
-        memory.apply_item_markdown(
-            "mem-edit",
-            source.replace("Original body", "Stale edit"),
-            expected_revision=expected_revision,
-        )
-
-    assert memory.get("mem-edit")["content"] == "Concurrent update"
-
-
-def test_apply_item_markdown_rolls_back_all_state_on_store_failure():
-    """apply_item_markdown fully restores AgentMemory state if _replace_memory_item fails.
-
-    The test injects a failure inside the store() call that executes AFTER
-    delete_memory() completes, so that at least one real mutation has already
-    happened before the exception is raised.  This verifies the rollback path
-    inside _replace_memory_item is exercised through apply_item_markdown, not
-    just through import_data.
-    """
-    memory = _editable_memory()
-    original_item = deepcopy(memory.get("mem-edit"))
-    original_stats = deepcopy(memory.stats)
-    original_index = list(memory.memory_index)
-    original_stm = [item.memory_id for item in memory.short_term_memory]
-    original_vector_ids = deepcopy(memory._vector_ids)
-
-    source = memory.export_item_markdown("mem-edit")
-    edited = source.replace("Original body", "Replaced body")
-
-    # Patch store() so it succeeds (internally called by _replace_memory_item),
-    # but raises AFTER the new item is inserted into memory_items.
-    real_store = memory.store
-    call_count = 0
-
-    def fail_after_store(*args, **kwargs):
-        nonlocal call_count
-        call_count += 1
-        result = real_store(*args, **kwargs)
-        # Raise on the store() call made by _replace_memory_item (not any earlier call)
-        if call_count >= 1:
-            raise RuntimeError("simulated store failure after insert")
-        return result
-
-    with patch.object(memory, "store", side_effect=fail_after_store):
-        with pytest.raises(RuntimeError, match="simulated store failure"):
-            memory.apply_item_markdown("mem-edit", edited)
-
-    # All state must be identical to what it was before apply_item_markdown
-    assert memory.get("mem-edit") == original_item, (
-        "memory_items must be fully restored after rollback"
-    )
-    assert memory.stats == original_stats, (
-        "stats must be fully restored after rollback"
-    )
-    assert list(memory.memory_index) == original_index, (
-        "memory_index must be fully restored after rollback"
-    )
-    assert [item.memory_id for item in memory.short_term_memory] == original_stm, (
-        "short_term_memory must be fully restored after rollback"
-    )
-    assert memory._vector_ids == original_vector_ids, (
-        "vector_ids must be fully restored after rollback"
-    )
-    # The memory must still be readable and unchanged
-    assert memory.exists("mem-edit")
-    assert memory.get("mem-edit")["content"] == "Original body"
-    assert memory.count() == 1
@@ -9,10 +9,6 @@ import yaml
 import semantica.context.context_graph as context_graph_module
 from semantica.change_management.managers import TemporalVersionManager
 from semantica.context.context_graph import ContextEdge, ContextGraph, ContextNode
-from semantica.context.markdown import (
-    MarkdownRevisionConflictError,
-    markdown_document_revision,
-)


 def _read_markdown(path: Path):
@@ -715,135 +711,3 @@ def test_json_remains_default_and_unknown_format_is_rejected(tmp_path):

    with pytest.raises(ValueError, match="Unsupported context graph"):
        graph.save_to_file(tmp_path / "graph", format="html")
-
-
-def _edited_node_document(graph, node_id, **frontmatter_updates):
-    source = graph.export_node_markdown(node_id)
-    frontmatter, body = graph._parse_markdown_document(source, f"node {node_id!r}")
-    frontmatter.update(frontmatter_updates)
-    return graph._render_markdown_document(
-        frontmatter,
-        body.replace("Keep evidence.", "Keep verified evidence."),
-        f"node {node_id!r}",
-    )
-
-
-def test_single_node_markdown_export_and_apply_update_complete_node_state():
-    graph, _, _ = _sample_graph()
-    events = []
-    graph.mutation_callback = lambda *event: events.append(event)
-    before_edges = list(graph.edges)
-    document = _edited_node_document(
-        graph,
-        "policy/\u6771\u4eac",
-        type="Decision",
-        properties={"category": "retention", "reviewed": True},
-        metadata={"source": "editor"},
-        valid_from="2026-03-01T00:00:00+00:00",
-        valid_until="2028-01-01T00:00:00+00:00",
-    )
-
-    assert graph.apply_node_markdown("policy/\u6771\u4eac", document) is True
-    node = graph.nodes["policy/\u6771\u4eac"]
-    assert node.node_id == "policy/\u6771\u4eac"
-    assert node.node_type == "Decision"
-    assert node.content == "# Retention\n\nKeep verified evidence.\n---\n"
-    assert node.properties == {"category": "retention", "reviewed": True}
-    assert node.metadata == {"source": "editor"}
-    assert node.valid_from == "2026-03-01T00:00:00+00:00"
-    assert node.valid_until == "2028-01-01T00:00:00+00:00"
-    assert "policy/\u6771\u4eac" not in graph.node_type_index.get("Policy", set())
-    assert "policy/\u6771\u4eac" in graph.node_type_index["Decision"]
-    assert "policy/\u6771\u4eac" in graph._decisions
-    assert graph.edges == before_edges
-    assert [event[0] for event in events] == ["UPDATE_NODE"]
-    assert graph.export_node_markdown("policy/\u6771\u4eac") == document
-
-
-def test_single_node_markdown_transition_out_of_decision_clears_indexes():
-    graph = ContextGraph(advanced_analytics=False)
-    graph.add_node("decision-1", "Decision", "Choose")
-    graph._rebuild_decision_indexes()
-    source = graph.export_node_markdown("decision-1")
-    document = source.replace("type: Decision", "type: Policy")
-
-    assert graph.apply_node_markdown("decision-1", document) is True
-    assert "decision-1" not in graph._decisions
-
-
-def test_single_node_markdown_invalid_identity_and_yaml_do_not_mutate():
-    graph, _, _ = _sample_graph()
-    events = []
-    graph.mutation_callback = lambda *event: events.append(event)
-    before = _normalized_state(graph)
-    source = graph.export_node_markdown("policy/\u6771\u4eac")
-
-    with pytest.raises(ValueError, match="does not match resource id"):
-        graph.apply_node_markdown(
-            "policy/\u6771\u4eac",
-            source.replace("id: policy/", "id: changed/"),
-        )
-    with pytest.raises(ValueError, match="Invalid Markdown frontmatter"):
-        graph.apply_node_markdown("policy/\u6771\u4eac", "---\nid: [\n---\n\nBroken")
-
-    assert _normalized_state(graph) == before
-    assert events == []
-
-
-def test_single_node_markdown_index_failure_rolls_back_complete_graph_state():
-    graph, _, _ = _sample_graph()
-    graph._analytics_cache["cached"] = {"score": 1.0}
-    events = []
-    graph.mutation_callback = lambda *event: events.append(event)
-    before = _normalized_state(graph)
-    before_type_index = {
-        node_type: set(node_ids)
-        for node_type, node_ids in graph.node_type_index.items()
-    }
-    before_analytics_cache = dict(graph._analytics_cache)
-    document = _edited_node_document(
-        graph,
-        "policy/\u6771\u4eac",
-        type="Decision",
-        properties={"confidence": {"invalid": True}},
-    )
-
-    with pytest.raises(TypeError):
-        graph.apply_node_markdown("policy/\u6771\u4eac", document)
-
-    assert _normalized_state(graph) == before
-    assert {
-        node_type: set(node_ids)
-        for node_type, node_ids in graph.node_type_index.items()
-    } == before_type_index
-    assert graph._analytics_cache == before_analytics_cache
-    assert not hasattr(graph, "_decisions")
-    assert events == []
-
-
-def test_single_node_markdown_noop_and_missing_node_are_safe():
-    graph, _, _ = _sample_graph()
-    events = []
-    graph.mutation_callback = lambda *event: events.append(event)
-    source = graph.export_node_markdown("policy/\u6771\u4eac")
-
-    assert graph.apply_node_markdown("policy/\u6771\u4eac", source) is False
-    with pytest.raises(KeyError, match="missing"):
-        graph.export_node_markdown("missing")
-    assert events == []
-
-
-def test_single_node_markdown_revision_check_is_atomic_with_apply():
-    graph, _, _ = _sample_graph()
-    source = graph.export_node_markdown("policy/\u6771\u4eac")
-    expected_revision = markdown_document_revision(source)
-    graph.add_node_attribute("policy/\u6771\u4eac", {"concurrent": True})
-
-    with pytest.raises(MarkdownRevisionConflictError):
-        graph.apply_node_markdown(
-            "policy/\u6771\u4eac",
-            source.replace("Keep evidence.", "Stale edit."),
-            expected_revision=expected_revision,
-        )
-
-    assert graph.nodes["policy/\u6771\u4eac"].properties["concurrent"] is True
@@ -247,18 +247,6 @@ class TestGraphNodes:
        assert payload["id"] == "python"
        assert payload["properties"]["content"] == "Python programming language"

-    def test_get_node_by_query_preserves_path_ids(self):
-        graph = ContextGraph(advanced_analytics=False)
-        graph.add_node("folder/node", node_type="note", content="Nested ID")
-        with TestClient(create_app(session=GraphSession(graph))) as test_client:
-            response = test_client.get(
-                "/api/graph/node",
-                params={"node_id": "folder/node"},
-            )
-
-        assert response.status_code == 200
-        assert response.json()["id"] == "folder/node"
-
    def test_get_neighbors(self, client):
        response = client.get("/api/graph/node/python/neighbors?depth=2")
        assert response.status_code == 200
@@ -60,22 +60,6 @@ def test_write_route_also_refuses_when_auth_not_configured(client, monkeypatch):
    assert resp.status_code == 503


-def test_markdown_write_route_requires_api_key(client, monkeypatch):
-    monkeypatch.delenv("SEMANTICA_ALLOW_ANONYMOUS", raising=False)
-    monkeypatch.setenv("SEMANTICA_API_KEY", "correct-key")
-
-    response = client.put(
-        "/api/markdown/context-node/python",
-        headers={"X-API-Key": "wrong-key"},
-        json={
-            "markdown": "---\nid: python\ntype: language\n---\n\nChanged",
-            "expected_revision": "sha256:" + ("0" * 64),
-        },
-    )
-
-    assert response.status_code == 401
-
-
 # ---------------------------------------------------------------------------
 # Configured key: wrong/missing key rejected, correct key accepted.
 # ---------------------------------------------------------------------------
@@ -1,135 +0,0 @@
-import pytest
-
-pytest.importorskip("fastapi")
-
-from fastapi import FastAPI  # noqa: E402
-from starlette.testclient import TestClient  # noqa: E402
-
-from semantica.context.context_graph import ContextGraph  # noqa: E402
-from semantica.explorer.runtime import install_mutation_bridge  # noqa: E402
-from semantica.explorer.session import GraphSession  # noqa: E402
-
-
-def test_mutation_bridge_supports_multiple_apps_for_one_graph(monkeypatch):
-    graph = ContextGraph(advanced_analytics=False)
-    first_session = GraphSession(graph)
-    second_session = GraphSession(graph)
-    received = []
-    graph.mutation_callback = lambda *event: received.append(("original", event))
-
-    monkeypatch.setattr(
-        first_session,
-        "handle_graph_mutation",
-        lambda *event: received.append(("first", event)),
-    )
-    monkeypatch.setattr(
-        second_session,
-        "handle_graph_mutation",
-        lambda *event: received.append(("second", event)),
-    )
-
-    first_app = FastAPI()
-    first_app.state.event_loop = None
-    first_app.state.ws_manager = None
-    second_app = FastAPI()
-    second_app.state.event_loop = None
-    second_app.state.ws_manager = None
-
-    install_mutation_bridge(first_app, first_session)
-    install_mutation_bridge(second_app, second_session)
-    graph.mutation_callback("UPDATE_NODE", "node-1", {"content": "Updated"})
-
-    assert [receiver for receiver, _ in received] == ["second", "first", "original"]
-
-
-def test_mutation_bridge_is_idempotent_for_one_app(monkeypatch):
-    graph = ContextGraph(advanced_analytics=False)
-    session = GraphSession(graph)
-    received = []
-    monkeypatch.setattr(
-        session,
-        "handle_graph_mutation",
-        lambda *event: received.append(event),
-    )
-    app = FastAPI()
-    app.state.event_loop = None
-    app.state.ws_manager = None
-
-    install_mutation_bridge(app, session)
-    install_mutation_bridge(app, session)
-    graph.mutation_callback("UPDATE_NODE", "node-1", {"content": "Updated"})
-
-    assert len(received) == 1
-
-
-def test_mutation_bridge_reinstalls_for_new_session_on_same_app(monkeypatch):
-    first_session = GraphSession(ContextGraph(advanced_analytics=False))
-    second_session = GraphSession(ContextGraph(advanced_analytics=False))
-    received = []
-    monkeypatch.setattr(
-        first_session,
-        "handle_graph_mutation",
-        lambda *event: received.append(("first", event)),
-    )
-    monkeypatch.setattr(
-        second_session,
-        "handle_graph_mutation",
-        lambda *event: received.append(("second", event)),
-    )
-    app = FastAPI()
-    app.state.event_loop = None
-    app.state.ws_manager = None
-
-    install_mutation_bridge(app, first_session)
-    install_mutation_bridge(app, second_session)
-    second_session.graph.mutation_callback(
-        "UPDATE_NODE",
-        "node-2",
-        {"content": "Updated"},
-    )
-
-    assert [receiver for receiver, _ in received] == ["second"]
-
-
-def test_legacy_server_mounts_editable_markdown_routes(monkeypatch):
-    monkeypatch.setenv("SEMANTICA_ALLOW_ANONYMOUS", "true")
-
-    from semantica import server
-
-    paths = {route.path for route in server.app.routes}
-    assert "/api/markdown/{kind}/{resource_id:path}" in paths
-    assert "/api/memories" in paths
-    assert "/ws/graph-updates" in paths
-
-    with TestClient(server.app) as client:
-        with client.websocket_connect("/ws/graph-updates") as websocket:
-            acknowledgement = websocket.receive_json()
-            assert acknowledgement["event"] == "connection_ack"
-            assert acknowledgement["data"] == {"connected": True}
-            assert acknowledgement["timestamp"]
-        info = client.get("/api/info")
-        memories = client.get("/api/memories")
-        server.app.state.session.graph.add_node(
-            "server-node",
-            "Note",
-            "Original server content",
-        )
-        current = client.get("/api/markdown/context-node/server-node").json()
-        saved = client.put(
-            "/api/markdown/context-node/server-node",
-            json={
-                "markdown": current["source"].replace(
-                    "Original server content",
-                    "Updated server content",
-                ),
-                "expected_revision": current["revision"],
-            },
-        )
-
-    assert info.json()["capabilities"]["agent_memory"] is False
-    assert memories.status_code == 503
-    assert memories.json()["detail"] == (
-        "AgentMemory is not configured for this Explorer instance."
-    )
-    assert saved.status_code == 200
-    assert saved.json()["body"] == "Updated server content"
@@ -1,319 +0,0 @@
-"""Integration tests for Explorer Markdown and memory selection routes."""
-
-import threading
-from datetime import datetime
-
-import pytest
-
-from semantica.context.agent_memory import AgentMemory
-from semantica.context.context_graph import ContextGraph
-
-pytest.importorskip("fastapi")
-
-from starlette.testclient import TestClient  # noqa: E402
-
-from semantica.explorer.app import create_app  # noqa: E402
-from semantica.explorer.session import GraphSession  # noqa: E402
-
-
-@pytest.fixture
-def markdown_client():
-    graph = ContextGraph(advanced_analytics=False)
-    graph.add_node("editable-node", "Note", "Original node")
-    events = []
-    graph.mutation_callback = lambda *event: events.append(event)
-    memory = AgentMemory()
-    memory.store(
-        "Original memory",
-        memory_id="editable-memory",
-        metadata={
-            "type": "note",
-            "updated_at": "2026-07-22T10:00:00+00:00",
-        },
-        timestamp=datetime.fromisoformat("2026-07-22T09:00:00+00:00"),
-    )
-    app = create_app(session=GraphSession(graph), agent_memory=memory)
-    with TestClient(app) as test_client:
-        yield test_client, graph, memory, events
-
-
-def test_gets_context_node_and_agent_memory(markdown_client):
-    client, _, _, _ = markdown_client
-
-    info = client.get("/api/info")
-    node = client.get("/api/markdown/context-node/editable-node")
-    memory = client.get("/api/markdown/agent-memory/editable-memory")
-
-    assert info.json()["capabilities"]["agent_memory"] is True
-    assert node.status_code == 200
-    assert node.json()["body"] == "Original node"
-    assert node.json()["resource"] == {
-        "kind": "context-node",
-        "id": "editable-node",
-    }
-    assert node.json()["source"].startswith("---\n")
-    assert node.json()["revision"].startswith("sha256:")
-    assert node.json()["editable"] is True
-    assert memory.status_code == 200
-    assert memory.json()["body"] == "Original memory"
-
-
-@pytest.mark.parametrize(
-    ("kind", "resource_id", "original", "updated"),
-    [
-        ("context-node", "editable-node", "Original node", "Updated node"),
-        ("agent-memory", "editable-memory", "Original memory", "Updated memory"),
-    ],
-)
-def test_put_updates_exact_resource(
-    markdown_client, kind, resource_id, original, updated
-):
-    client, graph, memory, _ = markdown_client
-    current = client.get(f"/api/markdown/{kind}/{resource_id}").json()
-
-    response = client.put(
-        f"/api/markdown/{kind}/{resource_id}",
-        json={
-            "markdown": current["source"].replace(original, updated),
-            "expected_revision": current["revision"],
-        },
-    )
-
-    assert response.status_code == 200
-    assert response.json()["changed"] is True
-    assert response.json()["body"] == updated
-    assert client.get(f"/api/markdown/{kind}/{resource_id}").json()["body"] == updated
-    if kind == "context-node":
-        assert graph.nodes[resource_id].content == updated
-        assert memory.get("editable-memory")["content"] == "Original memory"
-    else:
-        assert memory.get(resource_id)["content"] == updated
-        assert graph.nodes["editable-node"].content == "Original node"
-
-
-def test_validation_and_identity_errors_preserve_resource(markdown_client):
-    client, graph, _, events = markdown_client
-    current = client.get("/api/markdown/context-node/editable-node").json()
-
-    invalid = client.put(
-        "/api/markdown/context-node/editable-node",
-        json={
-            "markdown": "---\nid: [\n---\n\nBroken",
-            "expected_revision": current["revision"],
-        },
-    )
-    mismatch = client.put(
-        "/api/markdown/context-node/editable-node",
-        json={
-            "markdown": current["source"].replace(
-                "id: editable-node", "id: different-node"
-            ),
-            "expected_revision": current["revision"],
-        },
-    )
-
-    assert invalid.status_code == 422
-    assert invalid.json()["detail"]["code"] == "invalid_markdown_frontmatter"
-    assert "invalid YAML" in invalid.json()["detail"]["message"]
-    assert mismatch.status_code == 422
-    assert mismatch.json()["detail"] == {
-        "code": "resource_identity_mismatch",
-        "message": (
-            "Frontmatter id 'different-node' does not match resource id "
-            "'editable-node'."
-        ),
-        "field": "id",
-    }
-    assert graph.nodes["editable-node"].content == "Original node"
-    assert events == []
-
-
-def test_stale_revision_returns_conflict(markdown_client):
-    client, _, _, _ = markdown_client
-    current = client.get("/api/markdown/context-node/editable-node").json()
-    first = client.put(
-        "/api/markdown/context-node/editable-node",
-        json={
-            "markdown": current["source"].replace("Original node", "First update"),
-            "expected_revision": current["revision"],
-        },
-    )
-    stale = client.put(
-        "/api/markdown/context-node/editable-node",
-        json={
-            "markdown": current["source"].replace("Original node", "Stale update"),
-            "expected_revision": current["revision"],
-        },
-    )
-
-    assert first.status_code == 200
-    assert stale.status_code == 409
-    assert stale.json()["detail"]["code"] == "markdown_revision_conflict"
-    assert stale.json()["detail"]["current_revision"] == first.json()["revision"]
-
-
-def test_missing_and_failed_apply_are_structured(markdown_client, monkeypatch):
-    client, graph, _, _ = markdown_client
-    missing = client.get("/api/markdown/context-node/missing")
-    current = client.get("/api/markdown/context-node/editable-node").json()
-
-    def fail(_resource_id, _document):
-        raise RuntimeError("private storage failure")
-
-    monkeypatch.setattr(graph, "apply_node_markdown", fail)
-    failed = client.put(
-        "/api/markdown/context-node/editable-node",
-        json={
-            "markdown": current["source"].replace("Original node", "Will fail"),
-            "expected_revision": current["revision"],
-        },
-    )
-
-    assert missing.status_code == 404
-    assert missing.json()["detail"]["code"] == "markdown_resource_not_found"
-    assert failed.status_code == 500
-    assert failed.json()["detail"] == {
-        "code": "markdown_save_failed",
-        "message": "The edit could not be applied. The existing item was not changed.",
-    }
-    assert "private storage failure" not in failed.text
-
-
-def test_lists_memories_for_selection(markdown_client):
-    client, _, _, _ = markdown_client
-
-    response = client.get("/api/memories?skip=0&limit=100")
-
-    assert response.status_code == 200
-    assert response.json() == {
-        "items": [
-            {
-                "id": "editable-memory",
-                "type": "note",
-                "excerpt": "Original memory",
-                "updated_at": "2026-07-22T10:00:00+00:00",
-            }
-        ],
-        "total": 1,
-        "skip": 0,
-        "limit": 100,
-    }
-
-
-def test_memory_listing_is_atomic_with_concurrent_mutation(
-    markdown_client, monkeypatch
-):
-    client, _, memory, _ = markdown_client
-    snapshot_ready = threading.Event()
-    mutation_attempted = threading.Event()
-    mutation_finished = threading.Event()
-
-    def pause_after_key_snapshot(*, offset=0, limit=100, **_filters):
-        memory_ids = list(memory.memory_items.keys())[offset : offset + limit]
-        snapshot_ready.set()
-        assert mutation_attempted.wait(timeout=1)
-        mutation_finished.wait(timeout=0.25)
-
-        records = []
-        for memory_id in memory_ids:
-            # Match AgentMemory.list()'s second dictionary lookup after its
-            # key snapshot; this raises if a concurrent writer is not excluded.
-            memory.memory_items[memory_id]
-            record = memory.get_memory(memory_id)
-            if record is not None:
-                records.append(record)
-        return records
-
-    monkeypatch.setattr(memory, "list", pause_after_key_snapshot)
-
-    def delete_memory() -> None:
-        assert snapshot_ready.wait(timeout=1)
-        mutation_attempted.set()
-        memory.delete_memory("editable-memory")
-        mutation_finished.set()
-
-    writer = threading.Thread(target=delete_memory)
-    writer.start()
-    try:
-        response = client.get("/api/memories?skip=0&limit=100")
-    finally:
-        writer.join(timeout=2)
-
-    assert not writer.is_alive()
-    assert response.status_code == 200
-    assert [item["id"] for item in response.json()["items"]] == ["editable-memory"]
-    assert response.json()["total"] == 1
-
-
-def test_default_app_does_not_expose_agent_memory():
-    graph = ContextGraph(advanced_analytics=False)
-    with TestClient(create_app(session=GraphSession(graph))) as client:
-        info = client.get("/api/info")
-        memories = client.get("/api/memories")
-
-    assert info.json()["capabilities"]["agent_memory"] is False
-    assert memories.status_code == 503
-    assert memories.json()["detail"] == (
-        "AgentMemory is not configured for this Explorer instance."
-    )
-
-
-def test_slash_and_unicode_node_id_round_trip():
-    """GET and PUT work for node IDs containing '/' and Unicode characters.
-
-    Tests that:
-    - encodeURIComponent-style %2F encoding is transparent to the route
-    - the returned resource.id is the original unencoded string
-    - a successful PUT persists to the correct node
-    - the node ID is never rewritten by the apply path
-    """
-    node_id = "policy/\u6771\u4eac"  # "policy/東京"
-    graph = ContextGraph(advanced_analytics=False)
-    graph.add_node(node_id, "Policy", "Original slash body")
-    app = create_app(session=GraphSession(graph))
-
-    with TestClient(app) as client:
-        # GET via percent-encoded path (what encodeURIComponent produces)
-        import urllib.parse
-        encoded_id = urllib.parse.quote(node_id, safe="")
-        get_response = client.get(f"/api/markdown/context-node/{encoded_id}")
-
-        assert get_response.status_code == 200, (
-            f"GET returned {get_response.status_code}: {get_response.text}"
-        )
-        doc = get_response.json()
-        assert doc["resource"]["id"] == node_id, (
-            f"resource.id should be {node_id!r}, got {doc['resource']['id']!r}"
-        )
-        assert doc["resource"]["kind"] == "context-node"
-        assert doc["body"] == "Original slash body"
-        assert doc["revision"].startswith("sha256:")
-
-        # PUT an edit back via the same percent-encoded URL
-        updated_markdown = doc["source"].replace("Original slash body", "Updated slash body")
-        put_response = client.put(
-            f"/api/markdown/context-node/{encoded_id}",
-            json={
-                "markdown": updated_markdown,
-                "expected_revision": doc["revision"],
-            },
-        )
-
-        assert put_response.status_code == 200, (
-            f"PUT returned {put_response.status_code}: {put_response.text}"
-        )
-        result = put_response.json()
-        assert result["changed"] is True
-        assert result["body"] == "Updated slash body"
-        assert result["resource"]["id"] == node_id, (
-            f"PUT response resource.id should be {node_id!r}, got {result['resource']['id']!r}"
-        )
-
-        # Verify the live graph node was updated
-        assert graph.nodes[node_id].content == "Updated slash body"
-
-        # Also verify GET via literal slash URL works identically
-        get_literal = client.get(f"/api/markdown/context-node/{node_id}")
-        assert get_literal.status_code == 200
-        assert get_literal.json()["resource"]["id"] == node_id
-        assert get_literal.json()["body"] == "Updated slash body"
@@ -1,115 +0,0 @@
-from datetime import datetime
-
-import pytest
-
-from semantica.context.agent_memory import AgentMemory
-from semantica.context.context_graph import ContextGraph
-from semantica.explorer.markdown_resources import (
-    MarkdownResourceKind,
-    MarkdownResourceNotFound,
-    MarkdownResourceRef,
-    MarkdownResourceRegistry,
-    MarkdownRevisionConflict,
-    MarkdownSaveFailed,
-    document_revision,
-)
-
-
-def _resources():
-    graph = ContextGraph(advanced_analytics=False)
-    graph.add_node("node-1", "Note", "Original node")
-    graph.add_node("node-2", "Note", "Second node")
-    memory = AgentMemory()
-    memory.store(
-        "Original memory",
-        memory_id="mem-1",
-        timestamp=datetime.fromisoformat("2026-07-22T09:00:00+00:00"),
-        metadata={
-            "type": "note",
-            "updated_at": "2026-07-22T10:00:00+00:00",
-        },
-    )
-    return graph, memory, MarkdownResourceRegistry(graph, memory)
-
-
-def test_registry_routes_context_nodes_and_returns_canonical_revision():
-    graph, _, resources = _resources()
-    ref = MarkdownResourceRef(MarkdownResourceKind.CONTEXT_NODE, "node-1")
-
-    document = resources.read(ref)
-
-    assert document.body == "Original node"
-    assert document.revision == document_revision(document.source)
-    edited = document.source.replace("Original node", "Updated node")
-    result = resources.apply(ref, edited, document.revision)
-    assert result.changed is True
-    assert result.body == "Updated node"
-    assert graph.nodes["node-1"].content == "Updated node"
-
-
-def test_registry_routes_agent_memory_without_touching_context_graph():
-    graph, memory, resources = _resources()
-    ref = MarkdownResourceRef(MarkdownResourceKind.AGENT_MEMORY, "mem-1")
-    before_nodes = dict(graph.nodes)
-    document = resources.read(ref)
-
-    result = resources.apply(
-        ref,
-        document.source.replace("Original memory", "Updated memory"),
-        document.revision,
-    )
-
-    assert result.body == "Updated memory"
-    assert memory.get("mem-1")["content"] == "Updated memory"
-    assert graph.nodes == before_nodes
-
-
-def test_registry_rejects_stale_revision_and_preserves_current_state():
-    graph, _, resources = _resources()
-    ref = MarkdownResourceRef(MarkdownResourceKind.CONTEXT_NODE, "node-1")
-    first = resources.read(ref)
-    resources.apply(
-        ref,
-        first.source.replace("Original node", "First update"),
-        first.revision,
-    )
-
-    with pytest.raises(MarkdownRevisionConflict) as error:
-        resources.apply(
-            ref,
-            first.source.replace("Original node", "Stale update"),
-            first.revision,
-        )
-
-    assert error.value.current_revision == resources.read(ref).revision
-    assert graph.nodes["node-1"].content == "First update"
-
-
-def test_registry_missing_adapter_and_resources_are_structured():
-    graph, _, _ = _resources()
-    resources = MarkdownResourceRegistry(graph)
-
-    with pytest.raises(MarkdownResourceNotFound, match="not available"):
-        resources.read(MarkdownResourceRef(MarkdownResourceKind.AGENT_MEMORY, "mem-1"))
-    with pytest.raises(MarkdownResourceNotFound, match="missing"):
-        resources.read(
-            MarkdownResourceRef(MarkdownResourceKind.CONTEXT_NODE, "missing")
-        )
-
-
-def test_registry_does_not_expose_adapter_failure_details(monkeypatch):
-    graph, _, resources = _resources()
-    ref = MarkdownResourceRef(MarkdownResourceKind.CONTEXT_NODE, "node-1")
-    document = resources.read(ref)
-
-    def fail(_resource_id, _source):
-        raise RuntimeError("private backend failure")
-
-    monkeypatch.setattr(graph, "apply_node_markdown", fail)
-    with pytest.raises(MarkdownSaveFailed) as error:
-        resources.apply(ref, document.source + "changed", document.revision)
-
-    assert error.value.message == (
-        "The edit could not be applied. The existing item was not changed."
-    )
-    assert "private backend failure" not in error.value.message
@@ -1,308 +0,0 @@
-from types import SimpleNamespace
-
-import pytest
-
-from semantica.ontology import (
-    OntologyEngine,
-    OntologyQualityGate,
-    QualitySeverity,
-    ontology_quality_check,
-)
-
-
-def _ontology():
-    return {
-        "classes": [
-            {"name": "Person", "uri": "https://example.org/Person"},
-            {"name": "Company", "uri": "https://example.org/Company"},
-        ],
-        "properties": [
-            {
-                "name": "worksFor",
-                "type": "object",
-                "domain": ["Person"],
-                "range": ["Company"],
-            },
-            {
-                "name": "name",
-                "type": "data",
-                "domain": ["Person"],
-                "range": "string",
-            },
-        ],
-    }
-
-
-def test_quality_gate_reports_a_healthy_ontology():
-    report = ontology_quality_check(_ontology())
-
-    assert report.passed
-    assert report.metrics["coverage"] == 1.0
-    assert report.error_count == 0
-    assert report.to_dict()["stats"]["properties"] == 2
-
-
-def test_quality_gate_finds_schema_and_endpoint_problems():
-    ontology = {
-        "classes": [{"name": "Person"}, {"name": "Unused"}],
-        "properties": [
-            {
-                "name": "worksFor",
-                "type": "object",
-                "domain": ["Person"],
-                "range": ["MissingCompany"],
-            },
-            {"name": "unattached", "type": "data"},
-        ],
-    }
-    graph = {
-        "entities": [{"id": "p1", "type": "Person"}],
-        "relationships": [
-            {"source_id": "p1", "target_id": "missing", "type": "worksFor"}
-        ],
-    }
-
-    report = OntologyQualityGate().check(ontology, graph_data=graph)
-    codes = {issue.code for issue in report.issues}
-
-    assert not report.passed
-    assert "UNKNOWN_RANGE" in codes
-    assert "UNRESOLVED_RELATIONSHIP_ENDPOINT" in codes
-    assert "ORPHAN_CLASS" in codes
-    assert "MISSING_RANGE" in codes
-    assert any(issue.severity == QualitySeverity.WARNING for issue in report.issues)
-
-
-def test_quality_gate_supports_thresholds_and_legacy_endpoint_keys():
-    ontology = {
-        "classes": [{"name": "Person"}],
-        "properties": [
-            {
-                "name": "name",
-                "type": "data",
-                "domain": "Person",
-                "range": "xsd:string",
-            }
-        ],
-    }
-    graph = {
-        "entities": [{"entity_id": "p1", "type": "Person", "name": "Alice"}],
-        "relationships": [{"source": "p1", "target": "p1", "type": "knows"}],
-    }
-
-    report = ontology_quality_check(
-        ontology,
-        graph_data=graph,
-        thresholds={"min_coverage": 1.0},
-    )
-
-    assert report.passed
-    assert report.threshold_failures == []
-    assert report.stats["relationships"] == 1
-
-
-def test_quality_gate_can_fail_on_warnings():
-    report = ontology_quality_check(
-        {"classes": [{"name": "Person"}], "properties": []},
-        fail_on_warnings=True,
-    )
-
-    assert not report.passed
-    assert "fail_on_warnings" in report.threshold_failures
-
-
-def test_engine_exposes_quality_check():
-    report = OntologyEngine().quality_check(_ontology())
-
-    assert report.passed
-
-
-def test_quality_gate_accepts_canonical_context_graph_entities_without_mutation():
-    graph = {
-        "entities": [
-            {"id": "p1", "text": "Alice", "type": "Person"},
-            {"id": "c1", "text": "Acme", "type": "Company"},
-        ],
-        "relationships": [{"source_id": "p1", "target_id": "c1", "type": "worksFor"}],
-    }
-
-    report = OntologyQualityGate().check(_ontology(), graph_data=graph)
-
-    assert report.passed
-    assert "name" not in graph["entities"][0]
-
-
-def test_quality_gate_returns_structured_findings_for_malformed_graph_members():
-    report = OntologyQualityGate().check(
-        _ontology(), graph_data={"entities": [None], "relationships": [None]}
-    )
-    codes = {issue.code for issue in report.issues}
-
-    assert not report.passed
-    assert {"INVALID_ENTITY", "INVALID_RELATIONSHIP"} <= codes
-
-
-def test_quality_gate_returns_structured_finding_for_invalid_graph_containers():
-    report = OntologyQualityGate().check(
-        _ontology(), graph_data={"entities": None, "relationships": []}
-    )
-
-    assert not report.passed
-    assert any(issue.code == "INVALID_GRAPH" for issue in report.issues)
-
-
-def test_quality_gate_does_not_undercount_identical_dangling_edges():
-    graph = {
-        "entities": [{"id": "p1", "name": "Alice", "type": "Person"}],
-        "relationships": [
-            {"source": "p1", "target": "missing", "type": "knows"},
-            {"source": "p1", "target": "missing", "type": "knows"},
-        ],
-    }
-
-    report = OntologyQualityGate().check(
-        _ontology(), graph_data=graph, thresholds={"max_errors": 1}
-    )
-
-    endpoint_errors = [
-        issue
-        for issue in report.issues
-        if issue.code == "UNRESOLVED_RELATIONSHIP_ENDPOINT"
-    ]
-    assert len(endpoint_errors) == 2
-    assert not report.passed
-    assert "max_errors" in report.threshold_failures
-
-
-def test_quality_gate_indexes_all_class_identifier_aliases():
-    ontology = {
-        "classes": [{"name": "Person", "uri": "https://example.org/PersonType"}],
-        "properties": [
-            {
-                "name": "name",
-                "type": "data",
-                "domain": "https://example.org/PersonType",
-                "range": "string",
-            }
-        ],
-    }
-
-    report = OntologyQualityGate().check(ontology)
-    codes = {issue.code for issue in report.issues}
-
-    assert "UNKNOWN_DOMAIN" not in codes
-
-
-def test_quality_gate_recognizes_subclass_of_hierarchies():
-    ontology = {
-        "classes": [
-            {"name": "Person"},
-            {"name": "Employee", "subclassOf": "Person"},
-        ],
-        "properties": [
-            {
-                "name": "name",
-                "type": "data",
-                "domain": "Employee",
-                "range": "string",
-            }
-        ],
-    }
-
-    report = OntologyQualityGate().check(ontology)
-
-    assert not any(issue.code == "ORPHAN_CLASS" for issue in report.issues)
-
-
-def test_quality_gate_keeps_competency_evaluation_safe_for_malformed_members():
-    ontology = {
-        "classes": [None, {"uri": "https://example.org/Person"}],
-        "properties": [
-            None,
-            {
-                "uri": "https://example.org/name",
-                "type": "data",
-                "domain": "Person",
-                "range": "string",
-            },
-        ],
-    }
-
-    report = OntologyQualityGate().check(
-        ontology, competency_questions=["What is a person's name?"]
-    )
-
-    assert isinstance(report.metrics["competency_question_coverage"], float)
-
-
-def test_quality_gate_reports_validator_warnings_and_can_fail_on_them():
-    class WarningValidator:
-        def validate(self, ontology):
-            return SimpleNamespace(valid=True, errors=[], warnings=["review me"])
-
-    report = OntologyQualityGate(
-        validator=WarningValidator(), fail_on_warnings=True
-    ).check(_ontology())
-
-    assert report.warning_count == 1
-    assert "VALIDATOR_WARNING" in {issue.code for issue in report.issues}
-    assert "fail_on_warnings" in report.threshold_failures
-
-
-def test_quality_gate_isolates_competency_questions_between_checks():
-    engine = OntologyEngine()
-
-    first = engine.quality_check(_ontology(), competency_questions=["Who is a Person?"])
-    second = engine.quality_check(
-        _ontology(), competency_questions=["What is a location?"]
-    )
-
-    assert first.metrics["competency_question_coverage"] == 1.0
-    assert second.metrics["competency_question_coverage"] == 0.0
-
-
-def test_quality_gate_treats_null_property_type_as_missing():
-    ontology = {
-        "classes": [{"name": "Person"}],
-        "properties": [
-            {
-                "name": "value",
-                "type": None,
-                "domain": "Person",
-                "range": "string",
-            }
-        ],
-    }
-
-    report = OntologyQualityGate().check(ontology)
-
-    assert "MISSING_PROPERTY_TYPE" in {issue.code for issue in report.issues}
-    assert report.error_count >= 1
-
-
-def test_quality_gate_normalizes_orphan_ids_for_deterministic_reports():
-    graph = {
-        "entities": [
-            {"id": "p2", "name": "Bob", "type": "Person"},
-            {"id": "p1", "name": "Alice", "type": "Person"},
-        ],
-        "relationships": [],
-    }
-
-    report = OntologyQualityGate().check(_ontology(), graph_data=graph)
-    orphan = next(issue for issue in report.issues if issue.code == "ORPHAN_ENTITY")
-
-    assert orphan.details["ids"] == ["p1", "p2"]
-
-
-@pytest.mark.parametrize(
-    "thresholds",
-    [
-        {"min_coverage": float("nan")},
-        {"max_errors": float("inf")},
-        {"max_warnings": float("-inf")},
-    ],
-)
-def test_quality_gate_rejects_non_finite_thresholds(thresholds):
-    with pytest.raises(ValueError, match="finite"):
-        OntologyQualityGate().check(_ontology(), thresholds=thresholds)
Author	SHA1	Message	Date
Mohd Kaif	dd53b14e5d	Merge branch 'main' into fix/py39-install-deps	2026-09-03 22:43:31 +05:30
Zohaib Hassnain	2a70f5fcde	fix(deps): unblock python 3.9 core install	2026-09-03 21:48:07 +05:00