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)

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

@@ -192,7 +192,7 @@ class TestCollectionManager:
 
     @pytest.mark.asyncio
     async def test_update_document(self, collection_manager):
-        """Test updating a document."""
+        """Test updating a document with atomic replace."""
         result = await collection_manager.update_document(
             project_id="proj-123",
             agent_id="agent-456",
@@ -201,9 +201,10 @@ class TestCollectionManager:
             collection="default",
         )
 
-        # Should delete first, then ingest
-        collection_manager._database.delete_by_source.assert_called_once()
+        # Should use atomic replace (delete + insert in transaction)
+        collection_manager._database.replace_source_embeddings.assert_called_once()
         assert result.success is True
+        assert len(result.chunk_ids) == 1
 
     @pytest.mark.asyncio
     async def test_cleanup_expired(self, collection_manager):