Three methods on KnowledgeTable have no callers anywhere in the repository. get_knowledge_bases_by_user_id loaded every knowledge base and filtered them in Python, which search_knowledge_bases already does in SQL with pagination. get_knowledge_by_id_and_user_id duplicates check_access_by_user_id with the permission hardcoded to write. update_knowledge_data_by_id writes a data column that a migration dropped, so it could only ever raise and return None through its own except block.
What remains is one per-entry access helper and one SQL-filtered list path, so nobody reaches for the slower or the broken variant by accident.
No behaviour change.