refactor: thread explicit sessions through app retrieval paths (#38309)

Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>

api/core/tools/custom_tool/tool.py

@@ -6,6 +6,7 @@ from typing import Any, Union, override
 from urllib.parse import urlencode
 
 import httpx
+from sqlalchemy.orm import Session
 
 from core.helper import ssrf_proxy
 from core.tools.__base.tool import Tool
@@ -379,6 +380,7 @@ class ApiTool(Tool):
     @override
     def _invoke(
         self,
+        session: Session,
         user_id: str,
         tool_parameters: dict[str, Any],
         conversation_id: str | None = None,