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/config/paths.py

@@ -132,15 +132,20 @@ class Paths:
 
     @property
     def agents_dir(self) -> Path:
-        """Root directory for all custom agents: `{base_dir}/agents/`."""
+        """Legacy root for shared (pre user-isolation) custom agents: `{base_dir}/agents/`.
+
+        New code should use :meth:`user_agents_dir` instead. This property remains
+        only as a read-side fallback for installations that have not yet run the
+        ``migrate_user_isolation.py`` script.
+        """
         return self.base_dir / "agents"
 
     def agent_dir(self, name: str) -> Path:
-        """Directory for a specific agent: `{base_dir}/agents/{name}/`."""
+        """Legacy per-agent directory (no user isolation): `{base_dir}/agents/{name}/`."""
         return self.agents_dir / name.lower()
 
     def agent_memory_file(self, name: str) -> Path:
-        """Per-agent memory file: `{base_dir}/agents/{name}/memory.json`."""
+        """Legacy per-agent memory file: `{base_dir}/agents/{name}/memory.json`."""
         return self.agent_dir(name) / "memory.json"
 
     def user_dir(self, user_id: str) -> Path:
@@ -151,9 +156,17 @@ class Paths:
         """Per-user memory file: `{base_dir}/users/{user_id}/memory.json`."""
         return self.user_dir(user_id) / "memory.json"
 
+    def user_agents_dir(self, user_id: str) -> Path:
+        """Per-user root for that user's custom agents: `{base_dir}/users/{user_id}/agents/`."""
+        return self.user_dir(user_id) / "agents"
+
+    def user_agent_dir(self, user_id: str, agent_name: str) -> Path:
+        """Per-user per-agent directory: `{base_dir}/users/{user_id}/agents/{name}/`."""
+        return self.user_agents_dir(user_id) / agent_name.lower()
+
     def user_agent_memory_file(self, user_id: str, agent_name: str) -> Path:
         """Per-user per-agent memory: `{base_dir}/users/{user_id}/agents/{name}/memory.json`."""
-        return self.user_dir(user_id) / "agents" / agent_name.lower() / "memory.json"
+        return self.user_agent_dir(user_id, agent_name) / "memory.json"
 
     def thread_dir(self, thread_id: str, *, user_id: str | None = None) -> Path:
         """