Terminology Rename, and named-graphs for explainability (#682)

Terminology Rename, and named-graphs for explainability data

Changed terminology:
  - session -> question
  - retrieval -> exploration
  - selection -> focus
  - answer -> synthesis

- uris.py: Renamed query_session_uri → question_uri,
  retrieval_uri → exploration_uri, selection_uri → focus_uri,
  answer_uri → synthesis_uri
- triples.py: Renamed corresponding triple generation functions with
  updated labels ("GraphRAG question", "Exploration", "Focus",
  "Synthesis")
- namespaces.py: Added named graph constants GRAPH_DEFAULT,
  GRAPH_SOURCE, GRAPH_RETRIEVAL
- init.py: Updated exports
- graph_rag.py: Updated to use new terminology
- invoke_graph_rag.py: Updated CLI to display new stage names
  (Question, Exploration, Focus, Synthesis)

Query-Time Explainability → Named Graph
- triples.py: Added set_graph() helper function to set named graph
  on triples
- graph_rag.py: All explainability triples now use GRAPH_RETRIEVAL
  named graph
- rag.py: Explainability triples stored in user's collection (not
  separate collection) with named graph

Extraction Provenance → Named Graph
- relationships/extract.py: Provenance triples use GRAPH_SOURCE
  named graph
- definitions/extract.py: Provenance triples use GRAPH_SOURCE
  named graph
- chunker.py: Provenance triples use GRAPH_SOURCE named graph
- pdf_decoder.py: Provenance triples use GRAPH_SOURCE named graph

CLI Updates
- show_graph.py: Added -g/--graph option to filter by named graph and
  --show-graph to display graph column

Also:
- Fix knowledge core schemas

trustgraph-base/trustgraph/messaging/translators/retrieval.py

@@ -104,10 +104,10 @@ class GraphRagResponseTranslator(MessageTranslator):
         if explain_id:
             result["explain_id"] = explain_id
 
-        # Include explain_collection for explain messages
-        explain_collection = getattr(obj, "explain_collection", None)
-        if explain_collection:
-            result["explain_collection"] = explain_collection
+        # Include explain_graph for explain messages (named graph filter)
+        explain_graph = getattr(obj, "explain_graph", None)
+        if explain_graph is not None:
+            result["explain_graph"] = explain_graph
 
         # Include end_of_stream flag (LLM stream complete)
         result["end_of_stream"] = getattr(obj, "end_of_stream", False)