Enhance retrieval pipelines: 4-stage GraphRAG, DocRAG grounding (#697)

Enhance retrieval pipelines: 4-stage GraphRAG, DocRAG grounding,
consistent PROV-O

GraphRAG:
- Split retrieval into 4 prompt stages: extract-concepts,
  kg-edge-scoring,
  kg-edge-reasoning, kg-synthesis (was single-stage)
- Add concept extraction (grounding) for per-concept embedding
- Filter main query to default graph, ignoring
  provenance/explainability edges
- Add source document edges to knowledge graph

DocumentRAG:
- Add grounding step with concept extraction, matching GraphRAG's
  pattern:
  Question → Grounding → Exploration → Synthesis
- Per-concept embedding and chunk retrieval with deduplication

Cross-pipeline:
- Make PROV-O derivation links consistent: wasGeneratedBy for first
  entity from Activity, wasDerivedFrom for entity-to-entity chains
- Update CLIs (tg-invoke-agent, tg-invoke-graph-rag,
  tg-invoke-document-rag) for new explainability structure
- Fix all affected unit and integration tests

trustgraph-base/trustgraph/provenance/uris.py

@@ -68,6 +68,7 @@ def agent_uri(component_name: str) -> str:
 #
 # Terminology:
 #   Question    - What was asked, the anchor for everything
+#   Grounding   - Decomposing the question into concepts
 #   Exploration - Casting wide, what do we know about this space
 #   Focus       - Closing down, what's actually relevant here
 #   Synthesis   - Weaving the relevant pieces into an answer
@@ -87,6 +88,19 @@ def question_uri(session_id: str = None) -> str:
     return f"urn:trustgraph:question:{session_id}"
 
 
+def grounding_uri(session_id: str) -> str:
+    """
+    Generate URI for a grounding entity (concept decomposition of query).
+
+    Args:
+        session_id: The session UUID (same as question_uri).
+
+    Returns:
+        URN in format: urn:trustgraph:prov:grounding:{uuid}
+    """
+    return f"urn:trustgraph:prov:grounding:{session_id}"
+
+
 def exploration_uri(session_id: str) -> str:
     """
     Generate URI for an exploration entity (edges retrieved from subgraph).
@@ -173,6 +187,34 @@ def agent_iteration_uri(session_id: str, iteration_num: int) -> str:
     return f"urn:trustgraph:agent:{session_id}/i{iteration_num}"
 
 
+def agent_thought_uri(session_id: str, iteration_num: int) -> str:
+    """
+    Generate URI for an agent thought sub-entity.
+
+    Args:
+        session_id: The session UUID.
+        iteration_num: 1-based iteration number.
+
+    Returns:
+        URN in format: urn:trustgraph:agent:{uuid}/i{num}/thought
+    """
+    return f"urn:trustgraph:agent:{session_id}/i{iteration_num}/thought"
+
+
+def agent_observation_uri(session_id: str, iteration_num: int) -> str:
+    """
+    Generate URI for an agent observation sub-entity.
+
+    Args:
+        session_id: The session UUID.
+        iteration_num: 1-based iteration number.
+
+    Returns:
+        URN in format: urn:trustgraph:agent:{uuid}/i{num}/observation
+    """
+    return f"urn:trustgraph:agent:{session_id}/i{iteration_num}/observation"
+
+
 def agent_final_uri(session_id: str) -> str:
     """
     Generate URI for an agent final answer.
@@ -205,6 +247,19 @@ def docrag_question_uri(session_id: str = None) -> str:
     return f"urn:trustgraph:docrag:{session_id}"
 
 
+def docrag_grounding_uri(session_id: str) -> str:
+    """
+    Generate URI for a document RAG grounding entity (concept decomposition).
+
+    Args:
+        session_id: The session UUID.
+
+    Returns:
+        URN in format: urn:trustgraph:docrag:{uuid}/grounding
+    """
+    return f"urn:trustgraph:docrag:{session_id}/grounding"
+
+
 def docrag_exploration_uri(session_id: str) -> str:
     """
     Generate URI for a document RAG exploration entity (chunks retrieved).