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/tables/knowledge.py

@@ -233,7 +233,7 @@ class KnowledgeTableStore:
                     self.insert_triples_stmt,
                     (
                         uuid.uuid4(), m.metadata.user,
-                        m.metadata.id, when,
+                        m.metadata.root or m.metadata.id, when,
                         [], triples,
                     )
                 )
@@ -265,7 +265,7 @@ class KnowledgeTableStore:
                     self.insert_graph_embeddings_stmt,
                     (
                         uuid.uuid4(), m.metadata.user,
-                        m.metadata.id, when,
+                        m.metadata.root or m.metadata.id, when,
                         [], entities,
                     )
                 )
@@ -297,7 +297,7 @@ class KnowledgeTableStore:
                     self.insert_document_embeddings_stmt,
                     (
                         uuid.uuid4(), m.metadata.user,
-                        m.metadata.id, when,
+                        m.metadata.root or m.metadata.id, when,
                         [], chunks,
                     )
                 )