feat(agent): add custom-agent self-updates with user isolation (#2713)

* feat(agent): add update_agent tool for in-chat custom-agent self-updates (#2616)

Custom agents had no built-in way to persist updates to their own SOUL.md /
config.yaml from a normal chat — `setup_agent` was only bound during the
bootstrap flow, so when the user asked the agent to refine its description
or personality, the agent would shell out via bash/write_file and the edits
landed in a temporary sandbox/tool workspace instead of
`{base_dir}/agents/{agent_name}/`.

Changes:
- New `update_agent` builtin tool with partial-update semantics (only the
  fields you pass are written) and atomic temp-file + os.replace writes so
  a failed update never corrupts existing SOUL.md / config.yaml.
- Lead agent now binds `update_agent` in the non-bootstrap path whenever
  `agent_name` is set in the runtime context. Default agent (no
  agent_name) and bootstrap flow are unchanged.
- New `<self_update>` system-prompt section is injected for custom agents,
  instructing them to use `update_agent` — and explicitly NOT bash /
  write_file — to persist self-updates.
- Tests: 11 new cases in `tests/test_update_agent_tool.py` covering
  validation (missing/invalid agent_name, unknown agent, no fields),
  partial updates (soul-only, description-only, skills=[] vs omitted),
  no-op detection, atomic-write safety, and AgentConfig round-tripping;
  plus 2 new cases in `tests/test_lead_agent_prompt.py` covering the
  self-update prompt section.
- Docs: updated backend/CLAUDE.md builtin tools list and tools.mdx
  (en/zh) with the new tool description.

* feat(agent): isolate custom agents per user

Store custom agent definitions under the effective user, keep legacy agents readable until migration, and cover API/tool/migration behavior with tests.

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

* feat: consistent write/delete targets & add --user-id to migration

---------

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

backend/packages/harness/deerflow/agents/lead_agent/agent.py

@@ -318,7 +318,7 @@ def make_lead_agent(config: RunnableConfig):
 def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
     # Lazy import to avoid circular dependency
     from deerflow.tools import get_available_tools
-    from deerflow.tools.builtins import setup_agent
+    from deerflow.tools.builtins import setup_agent, update_agent
 
     cfg = _get_runtime_config(config)
     resolved_app_config = app_config
@@ -390,6 +390,9 @@ def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
             state_schema=ThreadState,
         )
 
+    # Custom agents can update their own SOUL.md / config via update_agent.
+    # The default agent (no agent_name) does not see this tool.
+    extra_tools = [update_agent] if agent_name else []
     # Default lead agent (unchanged behavior)
     return create_agent(
         model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled, reasoning_effort=reasoning_effort, app_config=resolved_app_config),
@@ -398,7 +401,8 @@ def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
             groups=agent_config.tool_groups if agent_config else None,
             subagent_enabled=subagent_enabled,
             app_config=resolved_app_config,
-        ),
+        )
+        + extra_tools,
         middleware=_build_middlewares(config, model_name=model_name, agent_name=agent_name, app_config=resolved_app_config),
         system_prompt=apply_prompt_template(
             subagent_enabled=subagent_enabled,