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/decoding/pdf/pdf_decoder.py

@@ -302,6 +302,7 @@ class Processor(FlowProcessor):
                 await flow("triples").send(Triples(
                     metadata=Metadata(
                         id=pg_uri,
+                        root=v.metadata.root,
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),
@@ -313,6 +314,7 @@ class Processor(FlowProcessor):
                 r = TextDocument(
                     metadata=Metadata(
                         id=pg_uri,
+                        root=v.metadata.root,
                         user=v.metadata.user,
                         collection=v.metadata.collection,
                     ),