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/skills/tool_policy.py

@@ -0,0 +1,44 @@
+import logging
+from typing import Protocol
+
+from deerflow.skills.types import Skill
+
+logger = logging.getLogger(__name__)
+
+
+class NamedTool(Protocol):
+    name: str
+
+
+def allowed_tool_names_for_skills(skills: list[Skill]) -> set[str] | None:
+    """Return the union of explicit skill allowed-tools declarations.
+
+    None means legacy allow-all behavior. It is returned only when no loaded
+    skill declares allowed-tools. Once any skill declares the field, legacy
+    skills without the field contribute no tools instead of disabling the
+    explicit restrictions from other skills.
+    """
+    if not skills:
+        return None
+
+    allowed: set[str] = set()
+    has_explicit_declaration = False
+    for skill in skills:
+        if skill.allowed_tools is None:
+            continue
+        has_explicit_declaration = True
+        if not skill.allowed_tools:
+            logger.info("Skill %s declared empty allowed-tools", skill.name)
+        allowed.update(skill.allowed_tools)
+
+    if not has_explicit_declaration:
+        return None
+    return allowed
+
+
+def filter_tools_by_skill_allowed_tools[ToolT: NamedTool](tools: list[ToolT], skills: list[Skill]) -> list[ToolT]:
+    allowed = allowed_tool_names_for_skills(skills)
+    if allowed is None:
+        return tools
+
+    return [tool for tool in tools if tool.name in allowed]