fix(core): address PR feedback regressions

Signed-off-by: phernandez <paul@basicmachines.co>

Author: phernandez

justfile

@@ -322,6 +322,15 @@ index-contract-test: file-index-runner-test file-index-batch-test file-index-sem
 runtime-core-pytest *args:
     BASIC_MEMORY_ENV=test uv run pytest -p pytest_mock -q --no-cov {{args}}
 
+# Focused PR #1002 Codex feedback regressions.
+pr-1002-feedback-test:
+    BASIC_MEMORY_ENV=test BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true LOGFIRE_IGNORE_NO_CONFIG=1 uv run pytest -p pytest_mock -q --no-cov \
+        tests/runtime/test_deleted_note_response.py \
+        tests/repository/test_accepted_note_search_repository.py \
+        tests/indexing/test_project_index_workflow.py \
+        tests/indexing/test_accepted_note_write_runner.py \
+        tests/indexing/test_directory_delete_runner.py
+
 runtime-core-fast-check-no-openai:
     OPENAI_API_KEY= just fast-check
 

src/basic_memory/index/local_dependencies.py

@@ -17,6 +17,7 @@
     BatchIndexer,
     CurrentMaterializedNoteEntityRepository,
     DefaultIndexBatchRuntime,
+    EmbeddingIndexBatchSummary,
     FileIndexOperation,
     FileIndexResult,
     IndexFileBatchIndexer,
@@ -116,6 +117,11 @@ class LocalIndexSearchService(
 ):
     """Search capabilities needed by local event/project indexing."""
 
+    async def sync_entity_vectors_batch(
+        self,
+        entity_ids: list[int],
+    ) -> EmbeddingIndexBatchSummary: ...
+
 
 class LocalIndexEntityService(Protocol):
     """Entity service capabilities needed by local index maintenance adapters."""

src/basic_memory/index/local_project.py

@@ -28,6 +28,7 @@
 )
 from basic_memory.indexing import (
     ChangeDetector,
+    EmbeddingBatchVectorSync,
     FileIndexChecker,
     IndexFileBatchJobResult,
     IndexFileBatchChecker,
@@ -165,6 +166,7 @@ class LocalProjectIndexRuntime:
     workflow_starter: ProjectIndexWorkflowStarter | None = None
     fanout_failure_recorder: ProjectIndexFanoutFailureRecorder | None = None
     completion_relation_runtime: RelationResolutionRuntime | None = None
+    embedding_vector_sync: EmbeddingBatchVectorSync | None = None
     batch_size: int = 100
     coordinator_job_id: RuntimeJobId | None = None
 
@@ -188,6 +190,16 @@ class LocalProjectIndexRuntimeProvider(Protocol):
     async def runtime_for_project(self, project: Project) -> LocalProjectIndexRuntime: ...
 
 
+def local_project_embedding_vector_sync(
+    dependencies: LocalIndexProjectDependencies,
+) -> EmbeddingBatchVectorSync | None:
+    """Return the semantic vector sync backend when local config enables it."""
+    app_config = dependencies.entity_service.app_config
+    if app_config is None or not app_config.semantic_search_enabled:
+        return None
+    return dependencies.search_service
+
+
 @dataclass(frozen=True, slots=True)
 class LocalIndexFileBatchReader(IndexFileBatchReader[IndexInputFile]):
     """Load current local files for the shared index-file batch runner."""
@@ -338,6 +350,7 @@ def runtime_from_dependencies(
                 link_resolver=dependencies.link_resolver,
                 entity_indexer=dependencies.search_service,
             ),
+            embedding_vector_sync=local_project_embedding_vector_sync(dependencies),
             batch_size=self.batch_size,
         )
 
@@ -416,6 +429,7 @@ async def run_local_project_index(
         batch_enqueuer=runtime.batch_enqueuer,
         fanout_failure_recorder=runtime.fanout_failure_recorder,
         batch_size=runtime.batch_size,
+        embedding_vector_sync=runtime.embedding_vector_sync,
     )
     if runtime.completion_relation_runtime is not None:
         await resolve_project_index_completion_relations(

src/basic_memory/indexing/accepted_note_write_runner.py

@@ -252,6 +252,12 @@ async def delete_entity(
         entity_id: RuntimeEntityId,
     ) -> None: ...
 
+    async def delete_entity_vectors(
+        self,
+        session: AsyncSession,
+        entity_id: RuntimeEntityId,
+    ) -> None: ...
+
 
 class AcceptedNoteWriteRepositories(Protocol):
     """Repository capability set needed by accepted-note DB-first writes."""
@@ -646,6 +652,19 @@ async def delete_accepted_note_search_index(
     await repository.delete_entity(session, entity_id)
 
 
+async def delete_accepted_note_vectors(
+    session: AsyncSession,
+    *,
+    project_id: ProjectId,
+    entity_id: RuntimeEntityId,
+    repositories: AcceptedNoteWriteRepositories | None = None,
+) -> None:
+    """Remove semantic vectors for an accepted-note entity inside the caller's transaction."""
+    write_repositories = repositories or build_default_accepted_note_write_repositories()
+    repository = write_repositories.search_repository(project_id)
+    await repository.delete_entity_vectors(session, entity_id)
+
+
 async def persist_accepted_note_write(
     session: AsyncSession,
     *,
@@ -721,5 +740,11 @@ async def delete_accepted_note(
             entity_id=entity.id,
             repositories=repositories,
         )
+        await delete_accepted_note_vectors(
+            session,
+            project_id=project_id,
+            entity_id=entity.id,
+            repositories=repositories,
+        )
         await session.delete(entity)
     return accepted

src/basic_memory/indexing/directory_delete_runner.py

@@ -10,6 +10,7 @@
 from sqlalchemy import bindparam, delete, select, text
 from sqlalchemy.ext.asyncio import AsyncSession
 
+from basic_memory.indexing.project_index_workflow import delete_project_index_vector_rows
 from basic_memory.models import Entity, NoteContent, Project
 from basic_memory.runtime import (
     RuntimeDirectoryFileSnapshot,
@@ -196,6 +197,11 @@ async def delete_directory_entities(
             ).bindparams(bindparam("entity_ids", expanding=True)),
             {"project_id": project_id, "entity_ids": tuple(entity_ids)},
         )
+        await delete_project_index_vector_rows(
+            session,
+            project_id=project_id,
+            entity_ids=tuple(entity_ids),
+        )
         await session.execute(delete(Entity).where(Entity.id.in_(entity_ids)))
 
 

src/basic_memory/indexing/project_index_workflow.py

@@ -17,6 +17,11 @@
     project_index_file_outcome_from_job_result,
 )
 from basic_memory.indexing.change_planning import ChangeReport
+from basic_memory.indexing.embedding_index_planning import (
+    EmbeddingBatchVectorSync,
+    EmbeddingIndexBatchJobRequest,
+    run_embedding_index_batch,
+)
 from basic_memory.indexing.project_index_progress import (
     ProjectIndexCompletion,
     ProjectIndexCounters,
@@ -1466,6 +1471,7 @@ async def run_project_index_coordinator(
     batch_enqueuer: ProjectIndexBatchEnqueuer,
     fanout_failure_recorder: ProjectIndexFanoutFailureRecorder | None,
     batch_size: int,
+    embedding_vector_sync: EmbeddingBatchVectorSync | None = None,
 ) -> ProjectIndexCoordinatorResult:
     """Run the storage-neutral project-index coordinator fan-out."""
     if not request.search:
@@ -1537,6 +1543,12 @@ async def run_project_index_coordinator(
             )
         raise
 
+    await sync_project_index_vector_targets(
+        request=request,
+        batch_results=batch_results,
+        embedding_vector_sync=embedding_vector_sync,
+    )
+
     return ProjectIndexCoordinatorResult(
         total_files=len(observed_files),
         enqueued_files=enqueued_files,
@@ -1551,6 +1563,34 @@ async def run_project_index_coordinator(
     )
 
 
+async def sync_project_index_vector_targets(
+    *,
+    request: RuntimeProjectIndexJobRequest,
+    batch_results: Sequence[IndexFileBatchJobResult],
+    embedding_vector_sync: EmbeddingBatchVectorSync | None,
+) -> None:
+    """Refresh vectors produced by inline project-index batch execution."""
+    if not request.embeddings or embedding_vector_sync is None:
+        return
+
+    vector_targets = tuple(
+        target for batch_result in batch_results for target in batch_result.vector_targets
+    )
+    if not vector_targets:
+        return
+
+    await run_embedding_index_batch(
+        EmbeddingIndexBatchJobRequest(
+            tenant_id=request.tenant_id,
+            project_id=request.project.project_id,
+            project_path=request.project.project_path,
+            entities=vector_targets,
+            workflow_id=request.workflow_id,
+        ),
+        vector_sync=embedding_vector_sync,
+    )
+
+
 def build_project_index_batch_activity_update(
     *,
     metadata: Mapping[str, object],

src/basic_memory/repository/accepted_note_search_repository.py

@@ -9,6 +9,7 @@
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from basic_memory.indexing.accepted_note_search import AcceptedNoteSearchRow
+from basic_memory.indexing.project_index_workflow import delete_project_index_vector_rows
 
 type SearchIndexSqlValue = str | int | datetime | None
 type SearchIndexSqlParams = dict[str, SearchIndexSqlValue]
@@ -31,7 +32,7 @@
         project_id
     ) VALUES (
         :id, :title, :content_stems, :content_snippet, :permalink, :file_path, :type,
-        CAST(:metadata AS jsonb),
+        :metadata,
         NULL, NULL, NULL,
         :entity_id, NULL,
         :created_at, :updated_at,
@@ -139,3 +140,15 @@ async def delete_entity(
             DELETE_ACCEPTED_NOTE_SEARCH_SQL,
             {"entity_id": entity_id, "project_id": self.project_id},
         )
+
+    async def delete_entity_vectors(
+        self,
+        session: AsyncSession,
+        entity_id: int,
+    ) -> None:
+        """Delete semantic vector rows for one accepted-note entity."""
+        await delete_project_index_vector_rows(
+            session,
+            project_id=self.project_id,
+            entity_ids=(entity_id,),
+        )

src/basic_memory/runtime/contracts.py

@@ -1017,9 +1017,8 @@ def from_entity(
                 field_name="title",
                 file_path=file_path,
             ),
-            permalink=required_runtime_deleted_note_text(
+            permalink=runtime_deleted_note_permalink(
                 entity.permalink,
-                field_name="permalink",
                 file_path=file_path,
             ),
         )
@@ -1108,6 +1107,21 @@ def required_runtime_deleted_note_text(
     return value.strip()
 
 
+def runtime_deleted_note_permalink(
+    value: object,
+    *,
+    file_path: RuntimeFilePath,
+) -> str:
+    """Return deleted-note permalink text, falling back to the file path."""
+    if isinstance(value, str) and value.strip():
+        return value.strip()
+
+    fallback = str(file_path).strip()
+    if not fallback:
+        raise RuntimeError(f"Deleted entity for {file_path} is missing permalink")
+    return fallback
+
+
 def runtime_deleted_note_reference_for_entity(
     entity: RuntimeDeletedNoteEntitySource,
     *,

tests/index/test_local_project_index.py

@@ -2106,6 +2106,20 @@ async def handle_delete(self, entity: Entity) -> None:
     async def index_entity(self, entity: Entity) -> None:
         return None
 
+    async def sync_entity_vectors_batch(
+        self,
+        entity_ids: list[int],
+    ) -> "RuntimeFactoryVectorBatchResult":
+        return RuntimeFactoryVectorBatchResult(entities_synced=len(entity_ids))
+
+
+@dataclass(frozen=True, slots=True)
+class RuntimeFactoryVectorBatchResult:
+    entities_synced: int
+    entities_skipped: int = 0
+    entities_failed: int = 0
+    entities_deferred: int = 0
+
 
 class RuntimeFactoryRelationRepository:
     async def find_unresolved_relations(

tests/indexing/test_accepted_note_mutation_runner.py

@@ -285,6 +285,7 @@ class _SearchRepository:
     def __init__(self) -> None:
         self.calls: list[tuple[AsyncSession, AcceptedNoteSearchRow]] = []
         self.deleted_entity_ids: list[int] = []
+        self.deleted_vector_entity_ids: list[int] = []
 
     async def refresh_entity(
         self,
@@ -301,6 +302,14 @@ async def delete_entity(
         _ = session
         self.deleted_entity_ids.append(entity_id)
 
+    async def delete_entity_vectors(
+        self,
+        session: AsyncSession,
+        entity_id: int,
+    ) -> None:
+        _ = session
+        self.deleted_vector_entity_ids.append(entity_id)
+
 
 @dataclass(frozen=True, slots=True)
 class _MutationLookupRepositories:
@@ -758,6 +767,7 @@ async def test_run_accepted_note_delete_removes_entity_and_returns_cleanup() ->
 
     assert session.deleted == [entity]
     assert search_repository.deleted_entity_ids == [entity.id]
+    assert search_repository.deleted_vector_entity_ids == [entity.id]
     assert change.status_code == 200
     assert change.file_delete is not None
     assert change.file_delete.file_path == "notes/accepted.md"