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/extract/kg/definitions/extract.py

@@ -20,7 +20,7 @@ from .... rdf import TRUSTGRAPH_ENTITIES, DEFINITION, RDF_LABEL, SUBJECT_OF
 from .... base import FlowProcessor, ConsumerSpec,  ProducerSpec
 from .... base import PromptClientSpec, ParameterSpec
 
-from .... provenance import statement_uri, triple_provenance_triples
+from .... provenance import statement_uri, triple_provenance_triples, set_graph, GRAPH_SOURCE
 from .... flow_version import __version__ as COMPONENT_VERSION
 
 DEFINITION_VALUE = Term(type=IRI, iri=DEFINITION)
@@ -175,6 +175,7 @@ class Processor(FlowProcessor):
                 triples.append(definition_triple)
 
                 # Generate provenance for the definition triple (reification)
+                # Provenance triples go in the source graph for separation from core knowledge
                 stmt_uri = statement_uri()
                 prov_triples = triple_provenance_triples(
                     stmt_uri=stmt_uri,
@@ -185,7 +186,7 @@ class Processor(FlowProcessor):
                     llm_model=llm_model,
                     ontology_uri=ontology_uri,
                 )
-                triples.extend(prov_triples)
+                triples.extend(set_graph(prov_triples, GRAPH_SOURCE))
 
                 # Link entity to chunk (not top-level document)
                 triples.append(Triple(

trustgraph-flow/trustgraph/extract/kg/relationships/extract.py

@@ -20,7 +20,7 @@ from .... rdf import RDF_LABEL, TRUSTGRAPH_ENTITIES, SUBJECT_OF
 from .... base import FlowProcessor, ConsumerSpec,  ProducerSpec
 from .... base import PromptClientSpec, ParameterSpec
 
-from .... provenance import statement_uri, triple_provenance_triples
+from .... provenance import statement_uri, triple_provenance_triples, set_graph, GRAPH_SOURCE
 from .... flow_version import __version__ as COMPONENT_VERSION
 
 RDF_LABEL_VALUE = Term(type=IRI, iri=RDF_LABEL)
@@ -162,6 +162,7 @@ class Processor(FlowProcessor):
                 triples.append(relationship_triple)
 
                 # Generate provenance for the relationship triple (reification)
+                # Provenance triples go in the source graph for separation from core knowledge
                 stmt_uri = statement_uri()
                 prov_triples = triple_provenance_triples(
                     stmt_uri=stmt_uri,
@@ -172,7 +173,7 @@ class Processor(FlowProcessor):
                     llm_model=llm_model,
                     ontology_uri=ontology_uri,
                 )
-                triples.extend(prov_triples)
+                triples.extend(set_graph(prov_triples, GRAPH_SOURCE))
 
                 # Label for s
                 triples.append(Triple(