diff --git a/docs/faq.md b/docs/faq.md
index c98fdf1c..3ce7c9a6 100644
--- a/docs/faq.md
+++ b/docs/faq.md
@@ -5,7 +5,7 @@ icon: "circle-question"
---
- Use **Ctrl+F** / **Cmd+F** to search this page. Common jumps: [Installation](#installation) · [Data & Features](#data--features) · [Troubleshooting](#troubleshooting)
+ Use **Ctrl+F** / **Cmd+F** to search this page. Common jumps: [Installation](#installation) · [Data & Features](#data-&-features) · [Troubleshooting](#troubleshooting)
## Quick Answers
diff --git a/docs/guides/agent-memory.md b/docs/guides/agent-memory.md
index 6954cf97..738f7b82 100644
--- a/docs/guides/agent-memory.md
+++ b/docs/guides/agent-memory.md
@@ -661,7 +661,7 @@ print("Total memories: {}".format(s.get("total_items", 0)))
- [Decision Intelligence](/guides/decision-intelligence) — Recording decisions as graph nodes with causal chains and policy gating.
- [Multi-Agent Systems](/guides/multi-agent) — Coordinating multiple agents through a shared `AgentContext` and save/load handoffs.
- [LLM Integrations](/guides/llm-integrations) — Configuring the LLM provider passed to `query_with_reasoning()`.
-- [Deduplication Guide](deduplication) — Full reference for `DuplicateDetector`, `EntityMerger`, similarity methods, and cluster strategies.
-- [Ontology Management](ontology) — Generate and validate OWL ontologies from the knowledge graph; export to Turtle, OWL/XML, JSON-LD.
+- [Deduplication Guide](/guides/deduplication) — Full reference for `DuplicateDetector`, `EntityMerger`, similarity methods, and cluster strategies.
+- [Ontology Management](/guides/ontology) — Generate and validate OWL ontologies from the knowledge graph; export to Turtle, OWL/XML, JSON-LD.
- [Context Module Reference](../reference/context) — Full API: `AgentContext`, `AgentMemory`, `MemoryItem`, `ContextRetriever`.
- [Vector Store Reference](../reference/vector_store) — FAISS, Qdrant, pgvector, Pinecone backends.
diff --git a/docs/guides/change-management.md b/docs/guides/change-management.md
index ae42e41c..76ee7e8d 100644
--- a/docs/guides/change-management.md
+++ b/docs/guides/change-management.md
@@ -497,7 +497,7 @@ print("Model v1.1 verified and approved for production.")
## Related Guides
- [Context Graphs](/guides/context-graphs) — `ContextGraph.to_dict()` feeds `create_snapshot()`
-- [Ontology Management](ontology) — pair ontology versioning with graph versioning for a complete schema + data audit trail
+- [Ontology Management](/guides/ontology) — pair ontology versioning with graph versioning for a complete schema + data audit trail
- [SHACL Validation](/guides/shacl-validation) — validate graph data at each version gate before snapshotting
-- [Provenance](provenance) — combine change management with W3C PROV-O lineage for a full audit trail
-- [Visualization](visualization) — `TemporalVisualizer.visualize_snapshot_comparison()` and `visualize_metrics_evolution()` render version diffs as interactive charts
+- [Provenance](/guides/provenance) — combine change management with W3C PROV-O lineage for a full audit trail
+- [Visualization](/guides/visualization) — `TemporalVisualizer.visualize_snapshot_comparison()` and `visualize_metrics_evolution()` render version diffs as interactive charts
diff --git a/docs/guides/conflict-resolution.md b/docs/guides/conflict-resolution.md
index 4c7becc7..49e074c6 100644
--- a/docs/guides/conflict-resolution.md
+++ b/docs/guides/conflict-resolution.md
@@ -65,7 +65,7 @@ flowchart TD
G --> H[SHACL Validation]
```
-1. **Deduplication** — Merge duplicate nodes so each entity has exactly one canonical record. Conflict resolution operates on a single canonical entity; you must identify it before comparing what different sources say about it. See [Deduplication](deduplication).
+1. **Deduplication** — Merge duplicate nodes so each entity has exactly one canonical record. Conflict resolution operates on a single canonical entity; you must identify it before comparing what different sources say about it. See [Deduplication](/guides/deduplication).
2. **Conflict Detection** — Call `detect_entity_conflicts()` to surface all property disagreements at once, or `detect_value_conflicts()` to target a specific property.
3. **Resolution** — For each conflict, apply a strategy (`CREDIBILITY_WEIGHTED`, `MOST_RECENT`, `VOTING`, etc.) or route it for expert review (`EXPERT_REVIEW`).
4. **Persist Canonical Values** — Write resolved values back to your canonical entities or graph store. See [Persisting resolved values](#persisting-resolved-values).
@@ -696,8 +696,8 @@ Calling `set_resolution_rule()` for every entity-property pair just to apply the
## Related Guides
-- [Deduplication](deduplication) — remove duplicate nodes before running conflict detection
-- [Provenance](provenance) — track which source each resolved value came from, and verify the audit trail cryptographically
+- [Deduplication](/guides/deduplication) — remove duplicate nodes before running conflict detection
+- [Provenance](/guides/provenance) — track which source each resolved value came from, and verify the audit trail cryptographically
- [SHACL Validation](/guides/shacl-validation) — enforce structural constraints after conflicts are resolved
- [Change Management](/guides/change-management) — snapshot the graph before and after conflict resolution runs
-- [Ontology Management](ontology) — align entity types to a shared vocabulary to reduce type conflicts at the schema level
+- [Ontology Management](/guides/ontology) — align entity types to a shared vocabulary to reduce type conflicts at the schema level
diff --git a/docs/guides/context-graphs.md b/docs/guides/context-graphs.md
index 9107c876..3f6e35a2 100644
--- a/docs/guides/context-graphs.md
+++ b/docs/guides/context-graphs.md
@@ -489,7 +489,7 @@ context2.load("agent_state/")
## Common Pitfalls
-**Duplicate entities.** Adding "APT-29", "APT29", and "Cozy Bear" as separate nodes fragments the graph when they should be one entity. Use consistent naming conventions upfront, or use `detect_duplicates()` and `EntityMerger` from the [Deduplication](deduplication) guide to merge them after ingestion.
+**Duplicate entities.** Adding "APT-29", "APT29", and "Cozy Bear" as separate nodes fragments the graph when they should be one entity. Use consistent naming conventions upfront, or use `detect_duplicates()` and `EntityMerger` from the [Deduplication](/guides/deduplication) guide to merge them after ingestion.
**Inconsistent naming conventions.** Mixing "ThreatActor", "threat_actor", and "Threat-Actor" as node types breaks queries that filter by type. Pick one convention and enforce it across all data sources.
@@ -706,8 +706,8 @@ for n in stress_reach:
- [Graph Analytics](/guides/graph-analytics) — centrality rankings, community detection, node embeddings, and link prediction on a populated `ContextGraph`
- [Decision Intelligence](/guides/decision-intelligence) — recording decisions as typed nodes, causal chain analysis, precedent search, and policy enforcement
-- [Ingest](ingest) — loading data from PDFs, APIs, databases, STIX bundles, and RSS feeds into the graph
-- [Deduplication](deduplication) — detecting and merging near-duplicate nodes before insertion to prevent graph fragmentation
-- [Reasoning](reasoning) — temporal interval algebra (Allen relations), forward/backward chaining, and SPARQL over the knowledge graph
-- [Ontology Management](ontology) — deriving formal OWL ontologies from `graph.to_dict()` for downstream reasoning engines
+- [Ingest](/guides/ingest) — loading data from PDFs, APIs, databases, STIX bundles, and RSS feeds into the graph
+- [Deduplication](/guides/deduplication) — detecting and merging near-duplicate nodes before insertion to prevent graph fragmentation
+- [Reasoning](/guides/reasoning) — temporal interval algebra (Allen relations), forward/backward chaining, and SPARQL over the knowledge graph
+- [Ontology Management](/guides/ontology) — deriving formal OWL ontologies from `graph.to_dict()` for downstream reasoning engines
- [Context Module Reference](../reference/context) — full API for `AgentContext`, `ContextGraph`, `ContextNode`, `ContextEdge`
diff --git a/docs/guides/decision-intelligence.md b/docs/guides/decision-intelligence.md
index 9053e778..e097c20e 100644
--- a/docs/guides/decision-intelligence.md
+++ b/docs/guides/decision-intelligence.md
@@ -664,6 +664,6 @@ results = context.find_precedents("APT29 infrastructure attribution", limit=5)
- [Context Graphs](/guides/context-graphs) — how `ContextGraph` stores decision nodes and causal edges
- [Distance Intelligence](/guides/distance-intelligence) — `trace_decision_causality()` annotates causal chains with confidence decay and distance bands
-- [Provenance](provenance) — W3C PROV-O audit trail that wraps decision records in standards-compliant provenance
+- [Provenance](/guides/provenance) — W3C PROV-O audit trail that wraps decision records in standards-compliant provenance
- [MCP Server](/guides/mcp-server) — expose decision recording and precedent search to LLM agents via the `record_decision` and `find_precedents` tools
- [Change Management](/guides/change-management) — checkpoint decision state with `flush_checkpoint()` for versioned snapshots
diff --git a/docs/guides/deduplication.md b/docs/guides/deduplication.md
index ccbbd7c8..841a7278 100644
--- a/docs/guides/deduplication.md
+++ b/docs/guides/deduplication.md
@@ -611,8 +611,8 @@ The similarity threshold controls sensitivity. Start at 0.7 and examine false po
## Related Guides
-- [Ingest Anything](ingest) — multi-source ingestion creates the duplicates this module resolves
+- [Ingest Anything](/guides/ingest) — multi-source ingestion creates the duplicates this module resolves
- [Context Graphs](/guides/context-graphs) — store deduplicated entities directly in the knowledge graph
- [Conflict Resolution](/guides/conflict-resolution) — after merging, reconcile disagreeing property values on the canonical entity
-- [Provenance](provenance) — track merge lineage so every canonical entity traces back to its original sources
-- [Pipeline](pipeline) — chain ingest, deduplicate, and store as a `PipelineBuilder` workflow
+- [Provenance](/guides/provenance) — track merge lineage so every canonical entity traces back to its original sources
+- [Pipeline](/guides/pipeline) — chain ingest, deduplicate, and store as a `PipelineBuilder` workflow
diff --git a/docs/guides/distance-intelligence.md b/docs/guides/distance-intelligence.md
index ff70d1a7..132909c1 100644
--- a/docs/guides/distance-intelligence.md
+++ b/docs/guides/distance-intelligence.md
@@ -561,4 +561,4 @@ for chain in chains:
- [Graph Analytics](/guides/graph-analytics) — centrality, community detection, Node2Vec embeddings, link prediction
- [Agent Memory](/guides/agent-memory) — proximity-blended retrieval (`proximity_weight`) integrates distance intelligence into memory search
- [Decision Intelligence](/guides/decision-intelligence) — `trace_decision_causality()` for causal chains with distance annotations
-- [Reasoning & Rules](reasoning) — `TemporalReasoningEngine` for Allen interval algebra over time-bounded graph nodes
+- [Reasoning & Rules](/guides/reasoning) — `TemporalReasoningEngine` for Allen interval algebra over time-bounded graph nodes
diff --git a/docs/guides/export.md b/docs/guides/export.md
index 00efe308..125c70f8 100644
--- a/docs/guides/export.md
+++ b/docs/guides/export.md
@@ -444,7 +444,7 @@ For semantic reasoning and ontology work, OWL/XML is the format — it is the on
## Related Guides
- [Context Graphs](/guides/context-graphs) — the `ContextGraph` object whose `to_dict()` feeds all exports
-- [Ontology Management](ontology) — export OWL ontologies generated from your graph
-- [Reasoning & Rules](reasoning) — reasoning results can be exported as RDF triples
+- [Ontology Management](/guides/ontology) — export OWL ontologies generated from your graph
+- [Reasoning & Rules](/guides/reasoning) — reasoning results can be exported as RDF triples
- [Change Management](/guides/change-management) — snapshot a graph before exporting to prove the export was made from a verified state
-- [Pipeline](pipeline) — chain ingest, extract, and export in a single `PipelineBuilder`
+- [Pipeline](/guides/pipeline) — chain ingest, extract, and export in a single `PipelineBuilder`
diff --git a/docs/guides/graph-analytics.md b/docs/guides/graph-analytics.md
index c2fbb7bb..bbbcf580 100644
--- a/docs/guides/graph-analytics.md
+++ b/docs/guides/graph-analytics.md
@@ -539,6 +539,6 @@ print(f"\n{len(result['communities'])} exposure clusters "
## Related Guides
- [Context Graphs](/guides/context-graphs) — building and querying the underlying `ContextGraph`
-- [Visualization](visualization) — render centrality rankings and community clusters as interactive dashboards
+- [Visualization](/guides/visualization) — render centrality rankings and community clusters as interactive dashboards
- [Decision Intelligence](/guides/decision-intelligence) — link prediction and structural similarity applied to decision nodes
- [GraphRAG](/guides/graphrag) — using analytics results to ground LLM generation in the most contextually relevant subgraph
diff --git a/docs/guides/ingest.md b/docs/guides/ingest.md
index e6ecd359..dda9c31e 100644
--- a/docs/guides/ingest.md
+++ b/docs/guides/ingest.md
@@ -950,9 +950,9 @@ print(f"Compliance graph: {graph.stats()['node_count']} nodes, "
## Related Guides
-- [Pipeline](pipeline) — chain ingest steps with `PipelineBuilder` for automated, retryable, parallelised workflows
+- [Pipeline](/guides/pipeline) — chain ingest steps with `PipelineBuilder` for automated, retryable, parallelised workflows
- [Context Graphs](/guides/context-graphs) — storing and querying the entities you ingest as a typed property graph
- [Semantic Extraction](/guides/semantic-extraction) — NER, relation extraction, and triplet extraction from ingested text
-- [Provenance](provenance) — tracking the origin document, confidence score, and ingestion timestamp for every extracted entity
+- [Provenance](/guides/provenance) — tracking the origin document, confidence score, and ingestion timestamp for every extracted entity
- [Databricks Integration](../integrations/databricks) — Unity Catalog setup, PAT/OAuth M2M authentication, and lineage introspection
- [Snowflake Integration](../integrations/snowflake) — warehouse setup and password/key-pair/OAuth authentication
diff --git a/docs/guides/mcp-server.md b/docs/guides/mcp-server.md
index db0cfef6..a8ae073a 100644
--- a/docs/guides/mcp-server.md
+++ b/docs/guides/mcp-server.md
@@ -342,8 +342,8 @@ The result is a fully auditable credit decision trail with precedent links, read
## Related Guides
-- [Reasoning & Rules](reasoning) — the engine behind the `run_reasoning` tool
+- [Reasoning & Rules](/guides/reasoning) — the engine behind the `run_reasoning` tool
- [Decision Intelligence](/guides/decision-intelligence) — how decisions are stored as causal graph nodes
- [Context Graphs](/guides/context-graphs) — the graph that `add_entity` and `add_relationship` write to
-- [Export & Serialization](export) — all export formats available via `export_graph`
-- [Ontology Management](ontology) — generate OWL ontologies from the graph built via MCP
+- [Export & Serialization](/guides/export) — all export formats available via `export_graph`
+- [Ontology Management](/guides/ontology) — generate OWL ontologies from the graph built via MCP
diff --git a/docs/guides/ontology.md b/docs/guides/ontology.md
index 8d6dad70..517d3f2f 100644
--- a/docs/guides/ontology.md
+++ b/docs/guides/ontology.md
@@ -504,7 +504,7 @@ else:
## Related Guides
- [SHACL Validation](/guides/shacl-validation) — generate W3C SHACL constraint shapes from your ontology and validate live graph data against them
-- [Reasoning & Rules](reasoning) — apply forward/backward-chaining rules over your ontology to derive new facts
-- [Export & Serialization](export) — export graphs to RDF, GraphML, CSV, and Neo4j Cypher
+- [Reasoning & Rules](/guides/reasoning) — apply forward/backward-chaining rules over your ontology to derive new facts
+- [Export & Serialization](/guides/export) — export graphs to RDF, GraphML, CSV, and Neo4j Cypher
- [Semantic Extraction](/guides/semantic-extraction) — extract entities and relationships that feed ontology generation
- [Context Graphs](/guides/context-graphs) — the knowledge graph that ontology generation reads from
diff --git a/docs/guides/pipeline.md b/docs/guides/pipeline.md
index b11470f5..dbd478bf 100644
--- a/docs/guides/pipeline.md
+++ b/docs/guides/pipeline.md
@@ -718,7 +718,7 @@ print(f"Compliance delta update: {result.output}")
## Related Guides
-- [Ingest](ingest) — all source types for the ingest step: PDFs, APIs, databases, RSS feeds, STIX directories, and streams
+- [Ingest](/guides/ingest) — all source types for the ingest step: PDFs, APIs, databases, RSS feeds, STIX directories, and streams
- [Semantic Extraction](/guides/semantic-extraction) — NER, relation extraction, triplet extraction, and event detection for the extract step
- [Context Graphs](/guides/context-graphs) — building and querying the `ContextGraph` that the store step populates
-- [Provenance](provenance) — tracking the origin document, confidence score, and pipeline run ID for every extracted entity
+- [Provenance](/guides/provenance) — tracking the origin document, confidence score, and pipeline run ID for every extracted entity
diff --git a/docs/guides/policy-engine.md b/docs/guides/policy-engine.md
index c5e075a6..fc284518 100644
--- a/docs/guides/policy-engine.md
+++ b/docs/guides/policy-engine.md
@@ -663,8 +663,8 @@ print("Policy updated to v2.4.0")
## Related Guides
- [Decision Intelligence](/guides/decision-intelligence) — `record_decision()`, causal chains, and precedent search — the decisions that `check_compliance()` evaluates
-- [Reasoning & Rules](reasoning) — complement policy rules with formal inference for logical conflict detection
+- [Reasoning & Rules](/guides/reasoning) — complement policy rules with formal inference for logical conflict detection
- [SHACL Validation](/guides/shacl-validation) — enforce structural constraints on policy nodes themselves
- [Change Management](/guides/change-management) — version-snapshot the policy graph alongside the knowledge graph
-- [Provenance](provenance) — W3C PROV-O lineage for every policy decision and exception
+- [Provenance](/guides/provenance) — W3C PROV-O lineage for every policy decision and exception
- [MCP Server](/guides/mcp-server) — expose `record_decision` and `find_precedents` as MCP tools for AI agents
diff --git a/docs/guides/provenance.md b/docs/guides/provenance.md
index 03b88f21..ee460eee 100644
--- a/docs/guides/provenance.md
+++ b/docs/guides/provenance.md
@@ -661,5 +661,5 @@ Note: the banking example above passes `agent_id="credit_data_service_v2"` to `t
- [Semantic Extraction](/guides/semantic-extraction) — the NER and relation extraction pipeline that auto-generates provenance entries for every extracted entity
- [Conflict Resolution](/guides/conflict-resolution) — provenance property sources feed directly into conflict detection; every resolved value is traceable to its source
-- [Deduplication](deduplication) — merge operations are recorded in merge history; pair with provenance for a complete lineage from source to canonical entity
+- [Deduplication](/guides/deduplication) — merge operations are recorded in merge history; pair with provenance for a complete lineage from source to canonical entity
- [Provenance Reference](../reference/provenance) — full storage backend API, `InMemoryStorage`, `SQLiteStorage`, and `ProvenanceEntry` schema
diff --git a/docs/guides/reasoning.md b/docs/guides/reasoning.md
index b64081ee..f715be19 100644
--- a/docs/guides/reasoning.md
+++ b/docs/guides/reasoning.md
@@ -840,7 +840,7 @@ if proof:
- [Semantic Extraction](/guides/semantic-extraction) — extract the entities and relationships that populate the graph facts you reason over
- [GraphRAG](/guides/graphrag) — retrieve graph-grounded context for LLM responses
-- [Ontology Management](ontology) — generate OWL ontologies to give your rules formal semantics
+- [Ontology Management](/guides/ontology) — generate OWL ontologies to give your rules formal semantics
- [Decision Intelligence](/guides/decision-intelligence) — record and trace inferred decisions through the full causal chain
- [Context Graphs](/guides/context-graphs) — the knowledge graph that reasoning operates over
- [MCP Server](/guides/mcp-server) — expose `run_reasoning` as a tool for Claude and other agents
diff --git a/docs/guides/semantic-extraction.md b/docs/guides/semantic-extraction.md
index c4c1fd11..6064d944 100644
--- a/docs/guides/semantic-extraction.md
+++ b/docs/guides/semantic-extraction.md
@@ -71,7 +71,7 @@ This pipeline transforms documents like "APT29 deployed HAMMERTOSS malware targe
`semantica.semantic_extract` turns unstructured text into structured graph-ready output: it identifies named entities, extracts relationships between them, detects time-anchored events, resolves coreferences, and serialises everything as RDF triplets. Use it to populate a `ContextGraph` from raw documents — intelligence reports, clinical notes, regulatory filings, or any free-text corpus.
- Extracted entities and relationships feed into `ContextGraph` via `AgentContext.store()`. For how they are attributed back to source documents, see the [Provenance Guide](provenance). For how the populated graph is queried and traversed, see [Context Graphs](/guides/context-graphs).
+ Extracted entities and relationships feed into `ContextGraph` via `AgentContext.store()`. For how they are attributed back to source documents, see the [Provenance Guide](/guides/provenance). For how the populated graph is queried and traversed, see [Context Graphs](/guides/context-graphs).
## Step 1 — Named Entity Recognition: who and what is in the text
@@ -668,9 +668,9 @@ The fallback behaviour is automatic: if the primary method returns an empty list
## Related Guides
-- [Provenance Guide](provenance) — track every extracted entity and chunk back to its source document
+- [Provenance Guide](/guides/provenance) — track every extracted entity and chunk back to its source document
- [Agent Memory Guide](/guides/agent-memory) — store extracted knowledge as searchable agent memories with graph enrichment
- [Context Graphs Guide](/guides/context-graphs) — how extracted entities populate `ContextGraph` nodes and edges
- [GraphRAG Guide](/guides/graphrag) — retrieve facts from the populated graph to ground LLM responses
-- [Reasoning Guide](reasoning) — derive new facts, run SPARQL queries, and apply inference rules over the extracted graph
+- [Reasoning Guide](/guides/reasoning) — derive new facts, run SPARQL queries, and apply inference rules over the extracted graph
- [Semantic Extract Reference](../reference/semantic_extract) — full API for all extractor classes, providers, and validators
diff --git a/docs/guides/shacl-validation.md b/docs/guides/shacl-validation.md
index df81df04..236b8994 100644
--- a/docs/guides/shacl-validation.md
+++ b/docs/guides/shacl-validation.md
@@ -753,8 +753,8 @@ def validate_before_publish(data_graph_str: str, ontology: dict) -> None:
## Related Guides
-- [Ontology Management](ontology) — generate the OWL ontology that SHACL shapes are derived from
-- [Reasoning & Rules](reasoning) — complement SHACL structural constraints with logical inference rules
-- [Export & Serialization](export) — serialize graph data to Turtle/RDF/XML for `run_shacl_validation` input
+- [Ontology Management](/guides/ontology) — generate the OWL ontology that SHACL shapes are derived from
+- [Reasoning & Rules](/guides/reasoning) — complement SHACL structural constraints with logical inference rules
+- [Export & Serialization](/guides/export) — serialize graph data to Turtle/RDF/XML for `run_shacl_validation` input
- [Conflict Resolution](/guides/conflict-resolution) — detect and resolve data conflicts before SHACL validation
- [Change Management](/guides/change-management) — version-gate SHACL shapes alongside ontology versions
diff --git a/docs/guides/visualization.md b/docs/guides/visualization.md
index 96a230ce..2efc2df1 100644
--- a/docs/guides/visualization.md
+++ b/docs/guides/visualization.md
@@ -615,7 +615,7 @@ fig.write_html("out.html") # manual export
## Related Guides
- [Context Graphs](/guides/context-graphs) — `graph.to_dict()` is the primary input for `KGVisualizer`
-- [Ontology Management](ontology) — `OntologyVisualizer` renders ontologies produced by `OntologyGenerator`
+- [Ontology Management](/guides/ontology) — `OntologyVisualizer` renders ontologies produced by `OntologyGenerator`
- [Change Management](/guides/change-management) — `TemporalVersionManager` snapshots feed `visualize_metrics_evolution()` and `visualize_snapshot_comparison()`
- [Graph Analytics](/guides/graph-analytics) — centrality scores, community dicts, and connectivity results that feed the `AnalyticsVisualizer`
-- [Export & Serialization](export) — export the same graph to GraphML, GEXF, or DOT for Gephi and Graphviz
+- [Export & Serialization](/guides/export) — export the same graph to GraphML, GEXF, or DOT for Gephi and Graphviz
diff --git a/docs/reference/change_management.md b/docs/reference/change_management.md
index ad74a54e..ee49b2a0 100644
--- a/docs/reference/change_management.md
+++ b/docs/reference/change_management.md
@@ -350,7 +350,7 @@ for record in history:
-- [Provenance](provenance) — W3C PROV-O lineage tracking.
+- [Provenance](/reference/provenance) — W3C PROV-O lineage tracking.
- [Knowledge Graph](/reference/kg) — The graph being versioned.
-- [Export](export) — Export versioned snapshots.
+- [Export](/reference/export) — Export versioned snapshots.
- [Conflicts](/reference/conflicts) — Detect conflicts introduced between versions.
diff --git a/docs/reference/conflicts.md b/docs/reference/conflicts.md
index b23cefe5..324fddaf 100644
--- a/docs/reference/conflicts.md
+++ b/docs/reference/conflicts.md
@@ -317,7 +317,7 @@ chain = tracker.get_traceability_chain("apple_inc")
- **Combine with provenance.** The `SourceTracker` feeds directly into the [Provenance](provenance) module's audit trail. If you need to explain how a resolved value was chosen, provenance records give you the full chain.
+ **Combine with provenance.** The `SourceTracker` feeds directly into the [Provenance](/reference/provenance) module's audit trail. If you need to explain how a resolved value was chosen, provenance records give you the full chain.
## ConflictAnalyzer
@@ -450,7 +450,7 @@ class InvestigationStep:
-- [Deduplication](deduplication) — Resolve duplicate entities before conflict detection.
-- [Ontology](ontology) — Logical conflicts use SHACL shapes and ontology axioms.
-- [Provenance](provenance) — Track which source each conflicting fact came from.
+- [Deduplication](/reference/deduplication) — Resolve duplicate entities before conflict detection.
+- [Ontology](/reference/ontology) — Logical conflicts use SHACL shapes and ontology axioms.
+- [Provenance](/reference/provenance) — Track which source each conflicting fact came from.
- [Knowledge Graph](/reference/kg) — The graph being checked for conflicts.
diff --git a/docs/reference/core.md b/docs/reference/core.md
index 741327f5..5fc8a6d9 100644
--- a/docs/reference/core.md
+++ b/docs/reference/core.md
@@ -226,7 +226,7 @@ result = build_knowledge_base(sources=["doc.pdf"], method="fast")
Use `Semantica` and `LifecycleManager` only when building a long-running application (e.g. a FastAPI service) that needs ordered startup, health checks, and graceful shutdown. For scripts and notebooks, use individual modules directly.
-- [Pipeline](pipeline) — Pipeline execution and step orchestration.
+- [Pipeline](/reference/pipeline) — Pipeline execution and step orchestration.
- [Utils](/reference/utils) — Shared utilities used by Core internally.
- [Getting Started](../getting-started) — Learn the basics before using Core.
- [LLMs](/reference/llms) — Configure LLM providers via ConfigManager.
diff --git a/docs/reference/deduplication.md b/docs/reference/deduplication.md
index d69f92ce..a6246acb 100644
--- a/docs/reference/deduplication.md
+++ b/docs/reference/deduplication.md
@@ -440,4 +440,4 @@ result = calculate_similarity(entity_a, entity_b, method="drug_name")
- [Conflicts](/reference/conflicts) — Detect value conflicts between non-duplicate entities.
- [Knowledge Graph](/reference/kg) — GraphBuilder uses deduplication during construction.
- [Normalize](/reference/normalize) — Normalize entity names before deduplication.
-- [Provenance](provenance) — Track merged entity lineage.
+- [Provenance](/reference/provenance) — Track merged entity lineage.
diff --git a/docs/reference/distance.md b/docs/reference/distance.md
index 1366e0fd..1e175c40 100644
--- a/docs/reference/distance.md
+++ b/docs/reference/distance.md
@@ -609,5 +609,5 @@ The Knowledge Explorer embeds Distance Intelligence directly in the browser dash
- [Context Module](/reference/context) — `ContextGraph.get_neighbors()` and proximity-blended retrieval.
- [Knowledge Graph Module](/reference/kg) — `NodeEmbedder`, `SimilarityCalculator`, and graph analytics.
-- [Visualization](visualization) — Programmatic distance heatmaps and ego-mode graph renders.
+- [Visualization](/reference/visualization) — Programmatic distance heatmaps and ego-mode graph renders.
- [Explorer](/reference/explorer) — Knowledge Explorer with built-in Distance Intelligence dashboard.
diff --git a/docs/reference/explorer.md b/docs/reference/explorer.md
index b24c3a18..a0f5b9bd 100644
--- a/docs/reference/explorer.md
+++ b/docs/reference/explorer.md
@@ -404,6 +404,6 @@ Semantic neighborhood requires node embeddings stored in node properties (keys `
Session state is in-memory only. Use `POST /api/export` to save a JSON snapshot before shutting down.
- [Context](/reference/context) — Build and save the ContextGraph that Explorer loads.
-- [Ontology](ontology) — Programmatic ontology management and SHACL generation.
-- [Visualization](visualization) — Programmatic graph rendering without the Explorer server.
-- [Export](export) — Export to RDF, Parquet, and other formats without launching a server.
+- [Ontology](/reference/ontology) — Programmatic ontology management and SHACL generation.
+- [Visualization](/reference/visualization) — Programmatic graph rendering without the Explorer server.
+- [Export](/reference/export) — Export to RDF, Parquet, and other formats without launching a server.
diff --git a/docs/reference/export.md b/docs/reference/export.md
index 61bf9cd6..2eb03533 100644
--- a/docs/reference/export.md
+++ b/docs/reference/export.md
@@ -395,6 +395,6 @@ The `export_csv` convenience function delegates to `CSVExporter.export()`. For p
- [Triplet Store](/reference/triplet_store) — Store RDF exports in a SPARQL-queryable backend.
-- [Ontology](ontology) — Export OWL ontologies.
-- [Provenance](provenance) — Include provenance metadata in RDF exports.
-- [Pipeline](pipeline) — Add export as a final pipeline step.
+- [Ontology](/reference/ontology) — Export OWL ontologies.
+- [Provenance](/reference/provenance) — Include provenance metadata in RDF exports.
+- [Pipeline](/reference/pipeline) — Add export as a final pipeline step.
diff --git a/docs/reference/graph_store.md b/docs/reference/graph_store.md
index 4c9b350a..82bd26ce 100644
--- a/docs/reference/graph_store.md
+++ b/docs/reference/graph_store.md
@@ -505,5 +505,5 @@ stats = store.get_stats()
- [KG Module](/reference/kg) — Build the graph before persisting it.
- [Triplet Store](/reference/triplet_store) — RDF triple store for semantic web and SPARQL queries.
-- [Visualization](visualization) — Visualize graphs stored in any backend.
+- [Visualization](/reference/visualization) — Visualize graphs stored in any backend.
- [Context](/reference/context) — AgentContext uses GraphStore for memory retrieval.
diff --git a/docs/reference/ingest.md b/docs/reference/ingest.md
index bb750179..c1e15b8e 100644
--- a/docs/reference/ingest.md
+++ b/docs/reference/ingest.md
@@ -647,7 +647,7 @@ result = ingest_file("source_path", method="my_format")
```
- [Parse](/reference/parse) — Parse raw sources into structured text and tables.
-- [Pipeline](pipeline) — Orchestrate ingest as the first pipeline step.
+- [Pipeline](/reference/pipeline) — Orchestrate ingest as the first pipeline step.
- [Snowflake Integration](../integrations/snowflake) — Snowflake-specific setup and authentication guide.
- [Databricks Integration](../integrations/databricks) — Databricks Unity Catalog setup, authentication, and lineage guide.
-- [Provenance](provenance) — Track lineage from ingest through to inference.
+- [Provenance](/reference/provenance) — Track lineage from ingest through to inference.
diff --git a/docs/reference/kg.md b/docs/reference/kg.md
index 31d80ed6..22789d3a 100644
--- a/docs/reference/kg.md
+++ b/docs/reference/kg.md
@@ -477,7 +477,7 @@ kg:
- [Graph Store](/reference/graph_store) — Persist graphs in Neo4j, FalkorDB, or Apache AGE.
- [Semantic Extract](/reference/semantic_extract) — Source of entities and relationships fed to GraphBuilder.
-- [Visualization](visualization) — Visualize knowledge graphs interactively.
+- [Visualization](/reference/visualization) — Visualize knowledge graphs interactively.
- [Conflicts](/reference/conflicts) — Conflict detection and resolution.
### Cookbooks
diff --git a/docs/reference/llms.md b/docs/reference/llms.md
index 365e5629..2692c4b9 100644
--- a/docs/reference/llms.md
+++ b/docs/reference/llms.md
@@ -27,7 +27,7 @@ from semantica.llms import Groq, OpenAI, LiteLLM, HuggingFaceLLM
| `HuggingFaceLLM` | Local HuggingFace Transformers | None (local) |
- **Anthropic, Gemini, Ollama, DeepSeek, Azure, Bedrock, Cohere, and 90+ others** are all available via `LiteLLM` using their model-string prefix. See the [LiteLLM section](#litellm-100-providers) below.
+ **Anthropic, Gemini, Ollama, DeepSeek, Azure, Bedrock, Cohere, and 90+ others** are all available via `LiteLLM` using their model-string prefix. See the [LiteLLM section](#litellm-100+-providers) below.
## What You Get
@@ -441,5 +441,5 @@ extractor = NERExtractor(
- [Semantic Extract](/reference/semantic_extract) — Use LLMs for NER and relation extraction.
- [Agno Integration](../integrations/agno) — LLM providers in Agno multi-agent teams.
-- [Reasoning](reasoning) — LLM-backed deductive and abductive reasoning.
+- [Reasoning](/reference/reasoning) — LLM-backed deductive and abductive reasoning.
- [Context](/reference/context) — GraphRAG uses LLMs for reasoning over knowledge graphs.
diff --git a/docs/reference/mcp_server.md b/docs/reference/mcp_server.md
index 37f63429..954aff70 100644
--- a/docs/reference/mcp_server.md
+++ b/docs/reference/mcp_server.md
@@ -495,5 +495,5 @@ The MCP server exposes three readable resources:
- [Context](/reference/context) — The ContextGraph that the MCP server operates on.
- [Semantic Extract](/reference/semantic_extract) — NER and relation extraction powering the MCP tools.
-- [Reasoning](reasoning) — Forward-chaining engine behind run_reasoning.
+- [Reasoning](/reference/reasoning) — Forward-chaining engine behind run_reasoning.
- [Agno Integration](../integrations/agno) — Use Semantica inside Agno multi-agent teams.
diff --git a/docs/reference/normalize.md b/docs/reference/normalize.md
index 4973eaeb..3765db9a 100644
--- a/docs/reference/normalize.md
+++ b/docs/reference/normalize.md
@@ -586,5 +586,5 @@ normalized = normalize_text("Apple Inc.", method="expand_suffixes")
- [Parse](/reference/parse) — Parse documents before normalization.
- [Split](/reference/split) — Chunk normalized text for embedding.
-- [Deduplication](deduplication) — Resolve duplicate entities after normalization.
-- [Pipeline](pipeline) — Include normalization as a named pipeline step.
+- [Deduplication](/reference/deduplication) — Resolve duplicate entities after normalization.
+- [Pipeline](/reference/pipeline) — Include normalization as a named pipeline step.
diff --git a/docs/reference/ontology.md b/docs/reference/ontology.md
index 5594e7de..889559c3 100644
--- a/docs/reference/ontology.md
+++ b/docs/reference/ontology.md
@@ -316,7 +316,7 @@ ontology_data = ingest_ontology("schema.jsonld") # JSON-LD
Ontology versioning (`VersionManager`, `OntologyVersion`) has moved to `semantica.change_management`. Import from there: `from semantica.change_management import VersionManager`.
-- [Reasoning](reasoning) — Apply inference rules over ontology axioms.
+- [Reasoning](/reference/reasoning) — Apply inference rules over ontology axioms.
- [Knowledge Graph](/reference/kg) — The graph being modeled by the ontology.
-- [Export](export) — Export ontologies as RDF, OWL, or JSON-LD.
+- [Export](/reference/export) — Export ontologies as RDF, OWL, or JSON-LD.
- [Conflicts](/reference/conflicts) — Detect ontology constraint violations.
diff --git a/docs/reference/parse.md b/docs/reference/parse.md
index a0673253..166c2072 100644
--- a/docs/reference/parse.md
+++ b/docs/reference/parse.md
@@ -297,7 +297,7 @@ for source in sources:
Docling is an optional dependency. If `docling` is not installed, `DoclingParser` raises an `ImportError` with installation instructions: `pip install docling`. `DocumentParser` is always available and requires no extras.
-- [Ingest](ingest) — Load files before parsing.
+- [Ingest](/reference/ingest) — Load files before parsing.
- [Split](/reference/split) — Chunk parsed text for embedding and extraction.
- [Docling Integration](../integrations/docling) — Full Docling integration setup guide.
- [Semantic Extract](/reference/semantic_extract) — Extract entities and relations from parsed text.
diff --git a/docs/reference/pipeline.md b/docs/reference/pipeline.md
index 9fe33aab..5097ceaf 100644
--- a/docs/reference/pipeline.md
+++ b/docs/reference/pipeline.md
@@ -588,7 +588,7 @@ StepStatus.SKIPPED # Skipped due to FailureHandler "skip" strategy
-- [Ingest](ingest) — First step in most pipelines.
+- [Ingest](/reference/ingest) — First step in most pipelines.
- [Semantic Extract](/reference/semantic_extract) — Core extraction step.
- [Knowledge Graph](/reference/kg) — Graph construction step.
-- [Export](export) — Final output step.
+- [Export](/reference/export) — Final output step.
diff --git a/docs/reference/provenance.md b/docs/reference/provenance.md
index edbc8026..e8f4ae51 100644
--- a/docs/reference/provenance.md
+++ b/docs/reference/provenance.md
@@ -523,6 +523,6 @@ Provenance tracking in Semantica produces the following audit artifacts:
- [Change Management](/reference/change_management) — Version control and snapshot audit trails.
-- [Ingest](ingest) — Provenance begins at the ingestion stage.
-- [Export](export) — Include provenance metadata in RDF exports.
+- [Ingest](/reference/ingest) — Provenance begins at the ingestion stage.
+- [Export](/reference/export) — Include provenance metadata in RDF exports.
- [Context](/reference/context) — Decision provenance via AgentContext.
diff --git a/docs/reference/reasoning.md b/docs/reference/reasoning.md
index 7c539d72..c56b5301 100644
--- a/docs/reference/reasoning.md
+++ b/docs/reference/reasoning.md
@@ -31,7 +31,7 @@ icon: "microchip"
## Which Engine Should I Use?
-- [Reasoner](#reasoner-forwardbackward-chaining) — IF/THEN rules, forward and backward chaining. **Start here**: covers 90% of use cases. No query language required.
+- [Reasoner](#reasoner-forward/backward-chaining) — IF/THEN rules, forward and backward chaining. **Start here**: covers 90% of use cases. No query language required.
- [GraphReasoner](#graphreasoner) — Natural language queries over a knowledge graph via LLM. No SPARQL or rules: just ask a question.
- [DatalogReasoner](#datalogreasoner) — Recursive Horn clause rules with guaranteed termination. Use for complex multi-hop transitive rules.
- [ReteEngine](#reteengine) — Rete pattern matching for high-frequency inference. Use when you need to match many facts against many rules simultaneously.
@@ -483,6 +483,6 @@ step.confidence # float
- [Knowledge Graph](/reference/kg) — The knowledge graph being reasoned over.
-- [Ontology](ontology) — Ontology axioms and SHACL constraints for logical reasoning.
+- [Ontology](/reference/ontology) — Ontology axioms and SHACL constraints for logical reasoning.
- [Triplet Store](/reference/triplet_store) — RDF backend for SPARQL-based reasoning.
- [Context](/reference/context) — Reasoning integrated into agent decision intelligence.
diff --git a/docs/reference/seed.md b/docs/reference/seed.md
index 736c7949..8313cbb8 100644
--- a/docs/reference/seed.md
+++ b/docs/reference/seed.md
@@ -321,7 +321,7 @@ export SEMANTICA_SEED_MERGE_STRATEGY=seed_first
**Use YAML configuration for production deployments.** Hard-coding source paths in Python scripts makes environment-switching (dev → staging → prod) fragile. Declare sources in `config.yaml` under the `seed:` key and override paths with `SEMANTICA_SEED_DATA_DIR`. This way, the same code runs in every environment.
-- [Ingest](ingest) — Load unstructured data alongside seed data.
+- [Ingest](/reference/ingest) — Load unstructured data alongside seed data.
- [Knowledge Graph](/reference/kg) — The target graph that seed data populates.
-- [Deduplication](deduplication) — Handle duplicates during seed-extracted merge.
-- [Pipeline](pipeline) — Incorporate seed loading as a named pipeline step.
+- [Deduplication](/reference/deduplication) — Handle duplicates during seed-extracted merge.
+- [Pipeline](/reference/pipeline) — Incorporate seed loading as a named pipeline step.
diff --git a/docs/reference/semantic_extract.md b/docs/reference/semantic_extract.md
index e8fbd9c0..d39ad093 100644
--- a/docs/reference/semantic_extract.md
+++ b/docs/reference/semantic_extract.md
@@ -448,4 +448,4 @@ triplets = trip.extract(text)
- [LLM Providers](/reference/llms) — Configure which LLM is used for extraction.
- [Knowledge Graph](/reference/kg) — Build graphs from extracted entities and relationships.
- [Parse Module](/reference/parse) — Parse documents before extraction.
-- [Deduplication](deduplication) — Resolve duplicate entities after extraction.
+- [Deduplication](/reference/deduplication) — Resolve duplicate entities after extraction.
diff --git a/docs/reference/split.md b/docs/reference/split.md
index 91d87306..66e3d037 100644
--- a/docs/reference/split.md
+++ b/docs/reference/split.md
@@ -371,9 +371,9 @@ for chunk in chunks:
print(f" {len(entities)} entities in chunk starting at {chunk.start_index}")
```
-For the full pipeline orchestration API, see the [Pipeline reference](pipeline).
+For the full pipeline orchestration API, see the [Pipeline reference](/reference/pipeline).
- [Parse](/reference/parse) — Parse documents before chunking: produces sections and metadata.
- [Embeddings](/reference/embeddings) — Embed chunks for vector search and semantic chunking.
- [Semantic Extract](/reference/semantic_extract) — Extract entities and relations from individual chunks.
-- [Pipeline](pipeline) — Integrate splitting as a named pipeline step.
+- [Pipeline](/reference/pipeline) — Integrate splitting as a named pipeline step.
diff --git a/docs/reference/temporal.md b/docs/reference/temporal.md
index f204d65d..71718c8d 100644
--- a/docs/reference/temporal.md
+++ b/docs/reference/temporal.md
@@ -876,8 +876,8 @@ kg:
- [Knowledge Graph Module](/reference/kg) — Core graph construction, `GraphBuilder`, analytics.
- [Context Module](/reference/context) — Decision temporal windows and `find_active_nodes()`.
-- [Provenance](provenance) — W3C PROV-O lineage stamped alongside temporal metadata.
-- [Export](export) — OWL, Turtle, JSON-LD, and Parquet export with temporal annotations.
+- [Provenance](/reference/provenance) — W3C PROV-O lineage stamped alongside temporal metadata.
+- [Export](/reference/export) — OWL, Turtle, JSON-LD, and Parquet export with temporal annotations.
- [Temporal Knowledge Graphs](https://github.com/semantica-agi/semantica/blob/main/cookbook/advanced/10_Temporal_Knowledge_Graphs.ipynb) — Temporal reasoning and Allen algebra · Advanced
- [Context Module](https://github.com/semantica-agi/semantica/blob/main/cookbook/introduction/19_Context_Module.ipynb) — Including temporal decision windows · Intermediate
diff --git a/docs/reference/triplet_store.md b/docs/reference/triplet_store.md
index 5be8c357..38d6ebec 100644
--- a/docs/reference/triplet_store.md
+++ b/docs/reference/triplet_store.md
@@ -561,7 +561,7 @@ for row in result.bindings:
print(row)
```
-- [Export](export) — Export knowledge graphs to RDF formats.
-- [Ontology](ontology) — Load OWL ontologies and store as RDF triples.
-- [Reasoning](reasoning) — SPARQL-based property chain inference.
+- [Export](/reference/export) — Export knowledge graphs to RDF formats.
+- [Ontology](/reference/ontology) — Load OWL ontologies and store as RDF triples.
+- [Reasoning](/reference/reasoning) — SPARQL-based property chain inference.
- [Graph Store](/reference/graph_store) — Property graph alternative for Cypher queries.
diff --git a/docs/reference/utils.md b/docs/reference/utils.md
index 2386a956..dadb59df 100644
--- a/docs/reference/utils.md
+++ b/docs/reference/utils.md
@@ -223,4 +223,4 @@ config = read_json_file("config.json")
```
- [Core](/reference/core) — Framework orchestration that uses Utils internally.
-- [Pipeline](pipeline) — Uses ProgressTracker for per-step tracking.
+- [Pipeline](/reference/pipeline) — Uses ProgressTracker for per-step tracking.
diff --git a/docs/reference/vector_store.md b/docs/reference/vector_store.md
index 2ca4b455..d5f9928e 100644
--- a/docs/reference/vector_store.md
+++ b/docs/reference/vector_store.md
@@ -591,4 +591,4 @@ store.create_index(index_type="pq", metric="L2", m=8)
- [Embeddings](/reference/embeddings) — Generate the vectors stored here.
- [Context](/reference/context) — AgentContext uses VectorStore for memory retrieval.
- [Split](/reference/split) — Chunk documents before embedding and storing.
-- [Ingest](ingest) — Ingest documents before embedding and storing.
+- [Ingest](/reference/ingest) — Ingest documents before embedding and storing.
diff --git a/docs/reference/visualization.md b/docs/reference/visualization.md
index 4ae9f59f..5e0d271c 100644
--- a/docs/reference/visualization.md
+++ b/docs/reference/visualization.md
@@ -291,6 +291,6 @@ semantica-explorer --graph my_graph.json
See the [Explorer reference](/reference/explorer) for the full feature set and REST API.
- [Knowledge Graph](/reference/kg) — The graph being visualized.
-- [Ontology](ontology) — Visualize ontology class structure.
+- [Ontology](/reference/ontology) — Visualize ontology class structure.
- [Embeddings](/reference/embeddings) — Generate the embeddings visualized here.
- [Explorer](/reference/explorer) — Full interactive Knowledge Explorer UI.