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

tests/unit/test_knowledge_graph/conftest.py

@@ -29,8 +29,9 @@ class Triple:
         self.o = o
 
 class Metadata:
-    def __init__(self, id, user, collection):
+    def __init__(self, id, user, collection, root=""):
         self.id = id
+        self.root = root
         self.user = user
         self.collection = collection