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/scripts/migrate_user_isolation.py

@@ -1,7 +1,7 @@
 """One-time migration: move legacy thread dirs and memory into per-user layout.
 
 Usage:
-    PYTHONPATH=. python scripts/migrate_user_isolation.py [--dry-run]
+    PYTHONPATH=. python scripts/migrate_user_isolation.py [--dry-run] [--user-id USER_ID]
 
 The script is idempotent — re-running it after a successful migration is a no-op.
 """
@@ -69,6 +69,67 @@ def migrate_thread_dirs(
     return report
 
 
+def migrate_agents(
+    paths: Paths,
+    user_id: str = "default",
+    *,
+    dry_run: bool = False,
+) -> list[dict]:
+    """Move legacy custom-agent directories into per-user layout.
+
+    Legacy layout:  ``{base_dir}/agents/{name}/``
+    Per-user layout: ``{base_dir}/users/{user_id}/agents/{name}/``
+
+    Pre-existing per-user agents take precedence: if a destination already
+    exists for an agent name, the legacy copy is moved to
+    ``{base_dir}/migration-conflicts/agents/{name}/`` for manual review.
+
+    Args:
+        paths: Paths instance.
+        user_id: Target user to receive the legacy agents (defaults to
+            ``"default"``, matching ``DEFAULT_USER_ID`` for no-auth setups).
+        dry_run: If True, only log what would happen.
+
+    Returns:
+        List of migration report entries, one per legacy agent directory found.
+    """
+    report: list[dict] = []
+    legacy_agents = paths.agents_dir
+    if not legacy_agents.exists():
+        logger.info("No legacy agents directory found — nothing to migrate.")
+        return report
+
+    for agent_dir in sorted(legacy_agents.iterdir()):
+        if not agent_dir.is_dir():
+            continue
+        agent_name = agent_dir.name
+        dest = paths.user_agent_dir(user_id, agent_name)
+
+        entry = {"agent": agent_name, "user_id": user_id, "action": ""}
+
+        if dest.exists():
+            conflicts_dir = paths.base_dir / "migration-conflicts" / "agents" / agent_name
+            entry["action"] = f"conflict -> {conflicts_dir}"
+            if not dry_run:
+                conflicts_dir.parent.mkdir(parents=True, exist_ok=True)
+                shutil.move(str(agent_dir), str(conflicts_dir))
+            logger.warning("Conflict for agent %s: moved legacy copy to %s", agent_name, conflicts_dir)
+        else:
+            entry["action"] = f"moved -> {dest}"
+            if not dry_run:
+                dest.parent.mkdir(parents=True, exist_ok=True)
+                shutil.move(str(agent_dir), str(dest))
+            logger.info("Migrated agent %s -> user %s", agent_name, user_id)
+
+        report.append(entry)
+
+    # Clean up empty legacy agents dir
+    if not dry_run and legacy_agents.exists() and not any(legacy_agents.iterdir()):
+        legacy_agents.rmdir()
+
+    return report
+
+
 def migrate_memory(
     paths: Paths,
     user_id: str = "default",
@@ -127,6 +188,12 @@ def _build_owner_map_from_db(paths: Paths) -> dict[str, str]:
 def main() -> None:
     parser = argparse.ArgumentParser(description="Migrate DeerFlow data to per-user layout")
     parser.add_argument("--dry-run", action="store_true", help="Log actions without making changes")
+    parser.add_argument(
+        "--user-id",
+        default="default",
+        metavar="USER_ID",
+        help=("User ID to claim un-owned legacy data (global memory.json and legacy custom agents). Defaults to 'default'. In multi-user installs, set this to the operator account that should inherit those legacy artifacts."),
+    )
     args = parser.parse_args()
 
     logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
@@ -134,26 +201,42 @@ def main() -> None:
     paths = get_paths()
     logger.info("Base directory: %s", paths.base_dir)
     logger.info("Dry run: %s", args.dry_run)
+    logger.info("Claiming un-owned legacy data for user_id=%s", args.user_id)
 
     owner_map = _build_owner_map_from_db(paths)
     logger.info("Found %d thread ownership records in DB", len(owner_map))
 
     report = migrate_thread_dirs(paths, owner_map, dry_run=args.dry_run)
-    migrate_memory(paths, user_id="default", dry_run=args.dry_run)
+    migrate_memory(paths, user_id=args.user_id, dry_run=args.dry_run)
+    agent_report = migrate_agents(paths, user_id=args.user_id, dry_run=args.dry_run)
 
     if report:
-        logger.info("Migration report:")
+        logger.info("Thread migration report:")
         for entry in report:
             logger.info("  thread=%s user=%s action=%s", entry["thread_id"], entry["user_id"], entry["action"])
     else:
         logger.info("No threads to migrate.")
 
+    if agent_report:
+        logger.info("Agent migration report:")
+        for entry in agent_report:
+            logger.info("  agent=%s user=%s action=%s", entry["agent"], entry["user_id"], entry["action"])
+    else:
+        logger.info("No agents to migrate.")
+
     unowned = [e for e in report if e["user_id"] == "default"]
     if unowned:
         logger.warning("%d thread(s) had no owner and were assigned to 'default':", len(unowned))
         for e in unowned:
             logger.warning("  %s", e["thread_id"])
 
+    if agent_report:
+        logger.warning(
+            "%d legacy agent(s) were assigned to '%s'. If those agents belonged to other users, move them manually under {base_dir}/users/<user_id>/agents/.",
+            len(agent_report),
+            args.user_id,
+        )
+
 
 if __name__ == "__main__":
     main()