fix(mcp-kb): add transactional batch insert and atomic document update

- Wrap store_embeddings_batch in transaction for all-or-nothing semantics
- Add replace_source_embeddings method for atomic document updates
- Update collection_manager to use transactional replace
- Prevents race conditions and data inconsistency (closes #77)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

mcp-servers/knowledge-base/tests/conftest.py

@@ -61,6 +61,7 @@ def mock_database():
     mock_db.delete_by_source = AsyncMock(return_value=1)
     mock_db.delete_collection = AsyncMock(return_value=5)
     mock_db.delete_by_ids = AsyncMock(return_value=2)
+    mock_db.replace_source_embeddings = AsyncMock(return_value=(1, ["new-id-1"]))
     mock_db.list_collections = AsyncMock(return_value=[])
     mock_db.get_collection_stats = AsyncMock()
     mock_db.cleanup_expired = AsyncMock(return_value=0)