fix(skills): enforce allowed-tools metadata (#2626)

* fix(skills): parse allowed-tools frontmatter

* fix(skills): validate allowed-tools metadata

* fix(skills): add shared allowed-tools policy

* fix(subagents): enforce skill allowed-tools

* fix(agent): enforce skill allowed-tools

* refactor(skills): dedupe TypeVar and reuse cached enabled skills

- Drop redundant module-level TypeVar in tool_policy; rely on PEP 695 syntax.
- Expose get_cached_enabled_skills() and have the lead agent reuse it
  instead of synchronously rescanning skills on every request.

* fix(agent): expose config-scoped skill cache

* fix(subagents): pass filtered tools explicitly

* fix(skills): clean allowed-tools policy feedback

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

@@ -20,6 +20,8 @@ from deerflow.agents.thread_state import ThreadState
 from deerflow.config.agents_config import load_agent_config, validate_agent_name
 from deerflow.config.app_config import AppConfig, get_app_config
 from deerflow.models import create_chat_model
+from deerflow.skills.tool_policy import filter_tools_by_skill_allowed_tools
+from deerflow.skills.types import Skill
 
 logger = logging.getLogger(__name__)
 
@@ -308,6 +310,28 @@ def _build_middlewares(
     return middlewares
 
 
+def _available_skill_names(agent_config, is_bootstrap: bool) -> set[str] | None:
+    if is_bootstrap:
+        return {"bootstrap"}
+    if agent_config and agent_config.skills is not None:
+        return set(agent_config.skills)
+    return None
+
+
+def _load_enabled_skills_for_tool_policy(available_skills: set[str] | None, *, app_config: AppConfig) -> list[Skill]:
+    try:
+        from deerflow.agents.lead_agent.prompt import get_enabled_skills_for_config
+
+        skills = get_enabled_skills_for_config(app_config)
+    except Exception:
+        logger.exception("Failed to load skills for allowed-tools policy")
+        raise
+
+    if available_skills is None:
+        return skills
+    return [skill for skill in skills if skill.name in available_skills]
+
+
 def make_lead_agent(config: RunnableConfig):
     """LangGraph graph factory; keep the signature compatible with LangGraph Server."""
     runtime_config = _get_runtime_config(config)
@@ -333,6 +357,7 @@ def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
     agent_name = validate_agent_name(cfg.get("agent_name"))
 
     agent_config = load_agent_config(agent_name) if not is_bootstrap else None
+    available_skills = _available_skill_names(agent_config, is_bootstrap)
     # Custom agent model from agent config (if any), or None to let _resolve_model_name pick the default
     agent_model_name = agent_config.model if agent_config and agent_config.model else None
 
@@ -371,15 +396,18 @@ def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
             "is_plan_mode": is_plan_mode,
             "subagent_enabled": subagent_enabled,
             "tool_groups": agent_config.tool_groups if agent_config else None,
-            "available_skills": ["bootstrap"] if is_bootstrap else (agent_config.skills if agent_config and agent_config.skills is not None else None),
+            "available_skills": sorted(available_skills) if available_skills is not None else None,
         }
     )
 
+    skills_for_tool_policy = _load_enabled_skills_for_tool_policy(available_skills, app_config=resolved_app_config)
+
     if is_bootstrap:
         # Special bootstrap agent with minimal prompt for initial custom agent creation flow
+        tools = get_available_tools(model_name=model_name, subagent_enabled=subagent_enabled, app_config=resolved_app_config) + [setup_agent]
         return create_agent(
             model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled, app_config=resolved_app_config),
-            tools=get_available_tools(model_name=model_name, subagent_enabled=subagent_enabled, app_config=resolved_app_config) + [setup_agent],
+            tools=filter_tools_by_skill_allowed_tools(tools, skills_for_tool_policy),
             middleware=_build_middlewares(config, model_name=model_name, app_config=resolved_app_config),
             system_prompt=apply_prompt_template(
                 subagent_enabled=subagent_enabled,
@@ -394,15 +422,10 @@ def _make_lead_agent(config: RunnableConfig, *, app_config: AppConfig):
     # The default agent (no agent_name) does not see this tool.
     extra_tools = [update_agent] if agent_name else []
     # Default lead agent (unchanged behavior)
+    tools = get_available_tools(model_name=model_name, groups=agent_config.tool_groups if agent_config else None, subagent_enabled=subagent_enabled, app_config=resolved_app_config)
     return create_agent(
         model=create_chat_model(name=model_name, thinking_enabled=thinking_enabled, reasoning_effort=reasoning_effort, app_config=resolved_app_config),
-        tools=get_available_tools(
-            model_name=model_name,
-            groups=agent_config.tool_groups if agent_config else None,
-            subagent_enabled=subagent_enabled,
-            app_config=resolved_app_config,
-        )
-        + extra_tools,
+        tools=filter_tools_by_skill_allowed_tools(tools + extra_tools, skills_for_tool_policy),
         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,