fix(core): apply create storage check to PUT-as-create branch

The PUT create-or-replace path creates a new entity when its external_id is
not yet in the DB, via prepare_create_or_reject, which also disabled the
storage existence check. Like POST create, this could commit DB/search rows
that diverge from an existing unindexed file on disk, which the next watcher
pass would overwrite. Thread verify_storage_absent_on_create through
prepare_create_or_reject and map the resulting EntityAlreadyExistsError to a
409 conflict so local PUT-as-create matches POST create. The replace branch
(entity already exists) is unchanged.

Follow-up to the #1002 review on accepted_note_mutation_runner create.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Signed-off-by: phernandez <paul@basicmachines.co>

Author: phernandez

src/basic_memory/indexing/accepted_note_mutation_runner.py

@@ -541,6 +541,7 @@ async def _run_accepted_note_update(
         prepared_write = await prepare_create_or_reject(
             preparer,
             request.data,
+            check_storage_exists=dependencies.verify_storage_absent_on_create,
             session=session,
         )
         entity = await create_accepted_pending_entity(
@@ -869,16 +870,21 @@ async def prepare_create_or_reject(
     preparer: AcceptedNoteCreatePreparer,
     data: EntitySchema,
     *,
+    check_storage_exists: bool,
     session: AsyncSession,
 ) -> AcceptedPreparedNoteWrite:
     """Prepare a new accepted note or raise a typed mutation rejection."""
     try:
         return await prepare_accepted_note_create(
             preparer,
             data,
-            check_storage_exists=False,
+            check_storage_exists=check_storage_exists,
             session=session,
         )
+    except EntityAlreadyExistsError as error:
+        # PUT-as-create over an unindexed on-disk file (local source-of-truth
+        # runtimes). Reject rather than committing divergent DB state.
+        reject_accepted_note_mutation(AcceptedNoteMutationRejectKind.conflict, str(error))
     except (ParseError, ValueError) as error:
         reject_accepted_note_mutation(AcceptedNoteMutationRejectKind.bad_request, str(error))
 

tests/api/v2/test_knowledge_router.py

@@ -419,6 +419,36 @@ async def test_create_entity_rejects_existing_unindexed_file(
     assert file_path.read_text(encoding="utf-8") == original
 
 
+@pytest.mark.asyncio
+async def test_put_create_rejects_existing_unindexed_file(
+    client: AsyncClient, v2_project_url, project_config
+):
+    """PUT-as-create over an unindexed on-disk file returns 409 (#1002 review).
+
+    The create branch of PUT (entity_id not in the DB) must apply the same
+    storage check as POST so it cannot commit DB/search state that diverges
+    from the file on disk.
+    """
+    file_path = project_config.home / "conflict" / "PutUnindexed.md"
+    file_path.parent.mkdir(parents=True, exist_ok=True)
+    original = "---\ntitle: PutUnindexed\ntype: note\n---\n\nPre-existing on-disk content\n"
+    file_path.write_text(original, encoding="utf-8")
+
+    new_external_id = "abcdef00-0000-4000-8000-000000000000"
+    response = await client.put(
+        f"{v2_project_url}/knowledge/entities/{new_external_id}",
+        json={
+            "title": "PutUnindexed",
+            "directory": "conflict",
+            "content": "New content via PUT",
+        },
+        params={"fast": False},
+    )
+
+    assert response.status_code == 409
+    assert file_path.read_text(encoding="utf-8") == original
+
+
 @pytest.mark.asyncio
 async def test_create_entity_returns_content(client: AsyncClient, file_service, v2_project_url):
     """Test creating an entity always returns file content with frontmatter."""