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-flow/trustgraph/decoding/pdf/pdf_decoder.py

@@ -24,6 +24,7 @@ from ... base import Consumer, Producer, ConsumerMetrics, ProducerMetrics
 
 from ... provenance import (
     document_uri, page_uri, derived_entity_triples,
+    set_graph, GRAPH_SOURCE,
 )
 
 # Component identification for provenance
@@ -285,7 +286,7 @@ class Processor(FlowProcessor):
                     title=f"Page {page_num}",
                 )
 
-                # Emit provenance triples
+                # Emit provenance triples (stored in source graph for separation from core knowledge)
                 doc_uri = document_uri(source_doc_id)
                 pg_uri = page_uri(source_doc_id, page_num)
 
@@ -305,7 +306,7 @@ class Processor(FlowProcessor):
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),
-                    triples=prov_triples,
+                    triples=set_graph(prov_triples, GRAPH_SOURCE),
                 ))
 
                 # Forward page document ID to chunker