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/persistence/repositories/run_repo.py

@@ -78,6 +78,7 @@ class RunRepository(RunStore):
         kwargs=None,
         error=None,
         created_at=None,
+        follow_up_to_run_id=None,
     ):
         now = datetime.now(UTC)
         row = RunRow(
@@ -90,6 +91,7 @@ class RunRepository(RunStore):
             metadata_json=self._safe_json(metadata) or {},
             kwargs_json=self._safe_json(kwargs) or {},
             error=error,
+            follow_up_to_run_id=follow_up_to_run_id,
             created_at=datetime.fromisoformat(created_at) if created_at else now,
             updated_at=now,
         )