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)

backend/app/gateway/services.py

@@ -266,6 +266,17 @@ async def start_run(
 
     disconnect = DisconnectMode.cancel if body.on_disconnect == "cancel" else DisconnectMode.continue_
 
+    # Resolve follow_up_to_run_id: explicit from request, or auto-detect from latest successful run
+    follow_up_to_run_id = getattr(body, "follow_up_to_run_id", None)
+    if follow_up_to_run_id is None:
+        run_store = get_run_store(request)
+        try:
+            recent_runs = await run_store.list_by_thread(thread_id, limit=1)
+            if recent_runs and recent_runs[0].get("status") == "success":
+                follow_up_to_run_id = recent_runs[0]["run_id"]
+        except Exception:
+            pass  # Don't block run creation
+
     try:
         record = await run_mgr.create_or_reject(
             thread_id,
@@ -274,6 +285,7 @@ async def start_run(
             metadata=body.metadata or {},
             kwargs={"input": body.input, "config": body.config},
             multitask_strategy=body.multitask_strategy,
+            follow_up_to_run_id=follow_up_to_run_id,
         )
     except ConflictError as exc:
         raise HTTPException(status_code=409, detail=str(exc)) from exc
@@ -302,17 +314,6 @@ async def start_run(
         except Exception:
             logger.warning("Failed to upsert thread_meta for %s (non-fatal)", thread_id)
 
-    # Resolve follow_up_to_run_id: explicit from request, or auto-detect from latest successful run
-    follow_up_to_run_id = getattr(body, "follow_up_to_run_id", None)
-    if follow_up_to_run_id is None:
-        run_store = get_run_store(request)
-        try:
-            recent_runs = await run_store.list_by_thread(thread_id, limit=1)
-            if recent_runs and recent_runs[0].get("status") == "success":
-                follow_up_to_run_id = recent_runs[0]["run_id"]
-        except Exception:
-            pass  # Don't block run creation
-
     agent_factory = resolve_agent_factory(body.assistant_id)
     graph_input = normalize_input(body.input)
     config = build_run_config(thread_id, body.config, body.metadata, assistant_id=body.assistant_id)