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/store/base.py

@@ -29,6 +29,7 @@ class RunStore(abc.ABC):
         kwargs: dict[str, Any] | None = None,
         error: str | None = None,
         created_at: str | None = None,
+        follow_up_to_run_id: str | None = None,
     ) -> None: ...
 
     @abc.abstractmethod
@@ -55,5 +56,24 @@ class RunStore(abc.ABC):
     @abc.abstractmethod
     async def delete(self, run_id: str) -> None: ...
 
+    @abc.abstractmethod
+    async def update_run_completion(
+        self,
+        run_id: str,
+        *,
+        status: str,
+        total_input_tokens: int = 0,
+        total_output_tokens: int = 0,
+        total_tokens: int = 0,
+        llm_call_count: int = 0,
+        lead_agent_tokens: int = 0,
+        subagent_tokens: int = 0,
+        middleware_tokens: int = 0,
+        message_count: int = 0,
+        last_ai_message: str | None = None,
+        first_human_message: str | None = None,
+        error: str | None = None,
+    ) -> None: ...
+
     @abc.abstractmethod
     async def list_pending(self, *, before: str | None = None) -> list[dict[str, Any]]: ...