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/messaging/translators/retrieval.py

@@ -84,6 +84,7 @@ class GraphRagRequestTranslator(MessageTranslator):
             triple_limit=int(data.get("triple-limit", 30)),
             max_subgraph_size=int(data.get("max-subgraph-size", 1000)),
             max_path_length=int(data.get("max-path-length", 2)),
+            edge_limit=int(data.get("edge-limit", 25)),
             streaming=data.get("streaming", False)
         )
 
@@ -96,6 +97,7 @@ class GraphRagRequestTranslator(MessageTranslator):
             "triple-limit": obj.triple_limit,
             "max-subgraph-size": obj.max_subgraph_size,
             "max-path-length": obj.max_path_length,
+            "edge-limit": obj.edge_limit,
             "streaming": getattr(obj, "streaming", False)
         }