fix(persistence): address review feedback on PR #1851

- Fix naive datetime.now() → datetime.now(UTC) in all ORM models
- Fix seq race condition in DbRunEventStore.put() with FOR UPDATE
  and UNIQUE(thread_id, seq) constraint
- Encapsulate _store access in RunManager.update_run_completion()
- Deduplicate _store.put() logic in RunManager via _persist_to_store()
- Add update_run_completion to RunStore ABC + MemoryRunStore
- Wire follow_up_to_run_id through the full create path
- Add error recovery to RunJournal._flush_sync() lost-event scenario
- Add migration note for search_threads breaking change
- Fix test_checkpointer_none_fix mock to set database=None

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

backend/app/gateway/routers/threads.py

@@ -317,7 +317,16 @@ async def create_thread(body: ThreadCreateRequest, request: Request) -> ThreadRe
 
 @router.post("/search", response_model=list[ThreadResponse])
 async def search_threads(body: ThreadSearchRequest, request: Request) -> list[ThreadResponse]:
-    """Search and list threads from the threads_meta table."""
+    """Search and list threads from the threads_meta table.
+
+    NOTE: Migration from pre-persistence-layer deployments:
+    Threads created via LangGraph Server before this change are NOT
+    automatically indexed in threads_meta. They will not appear in
+    search results until a new run is created on them (which triggers
+    thread_meta upsert in services.py). For bulk migration, run:
+      python -m deerflow.persistence.migrate_threads_from_checkpointer
+    (migration script TBD in a follow-up PR)
+    """
     from app.gateway.deps import get_thread_meta_repo
 
     repo = get_thread_meta_repo(request)