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/tools/builtins/setup_agent_tool.py

@@ -8,6 +8,7 @@ from langgraph.types import Command
 
 from deerflow.config.agents_config import validate_agent_name
 from deerflow.config.paths import get_paths
+from deerflow.runtime.user_context import get_effective_user_id
 
 logger = logging.getLogger(__name__)
 
@@ -34,7 +35,14 @@ def setup_agent(
     try:
         agent_name = validate_agent_name(agent_name)
         paths = get_paths()
-        agent_dir = paths.agent_dir(agent_name) if agent_name else paths.base_dir
+        if agent_name:
+            # Custom agents are persisted under the current user's bucket so
+            # different users do not see each other's agents.
+            user_id = get_effective_user_id()
+            agent_dir = paths.user_agent_dir(user_id, agent_name)
+        else:
+            # Default agent (no agent_name): SOUL.md lives at the global base dir.
+            agent_dir = paths.base_dir
         is_new_dir = not agent_dir.exists()
         agent_dir.mkdir(parents=True, exist_ok=True)