The id field in pipeline Metadata was being overwritten at each processing (#686)

The id field in pipeline Metadata was being overwritten at each processing
stage (document → page → chunk), causing knowledge storage to create
separate cores per chunk instead of grouping by document.

Add a root field that:
- Is set by librarian to the original document ID
- Is copied unchanged through PDF decoder, chunkers, and extractors
- Is used by knowledge storage for document_id grouping (with fallback to id)

Changes:
- Add root field to Metadata schema with empty string default
- Set root=document.id in librarian when initiating document processing
- Copy root through PDF decoder, recursive chunker, and all extractors
- Update knowledge storage to use root (or id as fallback) for grouping
- Add root handling to translators and gateway serialization
- Update test mock Metadata class to include root parameter

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

@@ -104,6 +104,7 @@ class Processor(FlowProcessor):
         tpls = Triples(
             metadata = Metadata(
                 id = metadata.id,
+                root = metadata.root,
                 user = metadata.user,
                 collection = metadata.collection,
             ),
@@ -116,6 +117,7 @@ class Processor(FlowProcessor):
         ecs = EntityContexts(
             metadata = Metadata(
                 id = metadata.id,
+                root = metadata.root,
                 user = metadata.user,
                 collection = metadata.collection,
             ),

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

@@ -218,6 +218,7 @@ class Processor(FlowProcessor):
                     flow("triples"),
                     Metadata(
                         id=v.metadata.id,
+                        root=v.metadata.root,
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),
@@ -231,6 +232,7 @@ class Processor(FlowProcessor):
                     flow("entity-contexts"),
                     Metadata(
                         id=v.metadata.id,
+                        root=v.metadata.root,
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),

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

@@ -554,6 +554,7 @@ class Processor(FlowProcessor):
         t = Triples(
             metadata=Metadata(
                 id=metadata.id,
+                root=metadata.root,
                 user=metadata.user,
                 collection=metadata.collection,
             ),
@@ -566,6 +567,7 @@ class Processor(FlowProcessor):
         ec = EntityContexts(
             metadata=Metadata(
                 id=metadata.id,
+                root=metadata.root,
                 user=metadata.user,
                 collection=metadata.collection,
             ),

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

@@ -219,6 +219,7 @@ class Processor(FlowProcessor):
                     flow("triples"),
                     Metadata(
                         id=v.metadata.id,
+                        root=v.metadata.root,
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),

trustgraph-flow/trustgraph/extract/kg/rows/processor.py

@@ -272,6 +272,7 @@ class Processor(FlowProcessor):
                     extracted = ExtractedObject(
                         metadata=Metadata(
                             id=f"{v.metadata.id}:{schema_name}",
+                            root=v.metadata.root,
                             user=v.metadata.user,
                             collection=v.metadata.collection,
                         ),