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/librarian/service.py

@@ -334,6 +334,7 @@ class Processor(AsyncProcessor):
             triples_msg = Triples(
                 metadata=Metadata(
                     id=doc_uri,
+                    root=document.id,
                     user=processing.user,
                     collection=processing.collection,
                 ),
@@ -380,6 +381,7 @@ class Processor(AsyncProcessor):
                 doc = TextDocument(
                     metadata = Metadata(
                         id = document.id,
+                        root = document.id,
                         user = processing.user,
                         collection = processing.collection
                     ),
@@ -390,6 +392,7 @@ class Processor(AsyncProcessor):
                 doc = TextDocument(
                     metadata = Metadata(
                         id = document.id,
+                        root = document.id,
                         user = processing.user,
                         collection = processing.collection
                     ),
@@ -405,6 +408,7 @@ class Processor(AsyncProcessor):
                 doc = Document(
                     metadata = Metadata(
                         id = document.id,
+                        root = document.id,
                         user = processing.user,
                         collection = processing.collection
                     ),
@@ -415,6 +419,7 @@ class Processor(AsyncProcessor):
                 doc = Document(
                     metadata = Metadata(
                         id = document.id,
+                        root = document.id,
                         user = processing.user,
                         collection = processing.collection
                     ),