fix(tools): introduce Runtime type alias to eliminate Pydantic serialization warning (#2774)

* fix(tools): introduce Runtime type alias to eliminate Pydantic serialization warning

Add deerflow/tools/types.py with:

    Runtime = ToolRuntime[dict[str, Any], ThreadState]

Replace every runtime: ToolRuntime[ContextT, ThreadState] and
runtime: ToolRuntime[dict[str, Any], ThreadState] annotation in
sandbox/tools.py, present_file_tool.py, task_tool.py, view_image_tool.py,
and skill_manage_tool.py with the new Runtime alias.

The unbound ContextT TypeVar (default None) caused
PydanticSerializationUnexpectedValue warnings on every tool call because
LangChain's BaseTool._parse_input calls model_dump() on the auto-generated
args_schema while DeerFlow passes a dict as runtime context.
Binding the context to dict[str, Any] aligns Pydantic's serialization
expectations with reality and removes the noise from all run modes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Cursor <cursoragent@cursor.com>

* fix(tools): extend Runtime alias to setup_agent and update_agent tools

Replace bare ToolRuntime annotations in setup_agent_tool.py and
update_agent_tool.py with the shared Runtime alias introduced in the
previous commit, and add both tools to the Pydantic serialization
warning regression test (13 cases total).

Co-authored-by: Cursor <cursoragent@cursor.com>

* test(tools): loosen Pydantic warning filter to avoid version-specific format

Replace the brittle "field_name='context'" substring check with a looser
"context" match so the assertion stays valid if Pydantic changes its
internal warning format across versions.

Co-authored-by: Cursor <cursoragent@cursor.com>

* test(tools): simplify warning filter and clean up docstring

Remove the "context" substring condition from the Pydantic warning
filter — asserting that no PydanticSerializationUnexpectedValue fires
at all is both simpler and more comprehensive, since the test payload
contains only the tool's own args plus runtime.

Also update the module docstring to remove the version-specific warning
format example that was inconsistent with the looser filter.

Co-authored-by: Cursor <cursoragent@cursor.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Cursor <cursoragent@cursor.com>

backend/packages/harness/deerflow/tools/skill_manage_tool.py

@@ -7,16 +7,15 @@ import logging
 from typing import Any
 from weakref import WeakValueDictionary
 
-from langchain.tools import ToolRuntime, tool
-from langgraph.typing import ContextT
+from langchain.tools import tool
 
 from deerflow.agents.lead_agent.prompt import refresh_skills_system_prompt_cache_async
-from deerflow.agents.thread_state import ThreadState
 from deerflow.mcp.tools import _make_sync_tool_wrapper
 from deerflow.skills.security_scanner import scan_skill_content
 from deerflow.skills.storage import get_or_new_skill_storage
 from deerflow.skills.storage.skill_storage import SkillStorage
 from deerflow.skills.types import SKILL_MD_FILE
+from deerflow.tools.types import Runtime
 
 logger = logging.getLogger(__name__)
 
@@ -31,7 +30,7 @@ def _get_lock(name: str) -> asyncio.Lock:
     return lock
 
 
-def _get_thread_id(runtime: ToolRuntime[ContextT, ThreadState] | None) -> str | None:
+def _get_thread_id(runtime: Runtime | None) -> str | None:
     if runtime is None:
         return None
     if runtime.context and runtime.context.get("thread_id"):
@@ -65,7 +64,7 @@ async def _to_thread(func, /, *args, **kwargs):
 
 
 async def _skill_manage_impl(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     action: str,
     name: str,
     content: str | None = None,
@@ -204,7 +203,7 @@ async def _skill_manage_impl(
 
 @tool("skill_manage", parse_docstring=True)
 async def skill_manage_tool(
-    runtime: ToolRuntime[ContextT, ThreadState],
+    runtime: Runtime,
     action: str,
     name: str,
     content: str | None = None,