fix(stabilization): harden attachment lifecycle and agent guard signals (#5420)

* fix: harden stabilization attachment and agent guards

* fix(uploads): preserve durable references during cleanup

* fix(uploads): close cleanup and compaction races

src/app_initializer.py

@@ -21,6 +21,7 @@ from src.model_discovery import ModelDiscovery
 from src.chat_handler import ChatHandler
 from src.research_handler import ResearchHandler
 from src.upload_handler import UploadHandler
+from src.tool_utils import set_upload_handler
 from src.search import update_search_config
 
 logger = logging.getLogger(__name__)
@@ -49,6 +50,8 @@ def initialize_managers(base_dir: str, rag_manager=None) -> Dict[str, Any]:
     session_manager = SessionManager(SESSIONS_FILE)
     set_session_manager(session_manager)  # Enable Session.add_message() persistence
     upload_handler = UploadHandler(base_dir, UPLOAD_DIR)
+    session_manager.upload_handler = upload_handler
+    set_upload_handler(upload_handler)
     personal_docs_manager = PersonalDocsManager(PERSONAL_DIR, rag_manager)
     api_key_manager = APIKeyManager(DATA_DIR)
     preset_manager = PresetManager(DATA_DIR)