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/packages/harness/deerflow/runtime/runs/worker.py

@@ -257,16 +257,8 @@ async def run_agent(
                 logger.warning("Failed to flush journal for run %s", run_id, exc_info=True)
 
             # Persist token usage + convenience fields to RunStore
-            if run_manager._store is not None:
-                try:
-                    completion = journal.get_completion_data()
-                    await run_manager._store.update_run_completion(
-                        run_id,
-                        status=record.status.value,
-                        **completion,
-                    )
-                except Exception:
-                    logger.warning("Failed to persist run completion for %s", run_id, exc_info=True)
+            completion = journal.get_completion_data()
+            await run_manager.update_run_completion(run_id, status=record.status.value, **completion)
 
         # Sync title from checkpoint to threads_meta.display_name
         if thread_meta_repo is not None and checkpointer is not None: