[FEATURE] Extend skillOverrides to plugin-namespaced skills

Preflight Checklist

• [x] I have searched existing requests
• [x] This is a single feature request

Problem Statement

Claude Code's skillOverrides setting supports on, name-only, user-invocable-only, and off, but explicitly excludes plugin skills.

This leaves users of multi-skill plugins with no way to remove one unwanted skill from Claude's context. Permission rules such as:

{
  "permissions": {
    "deny": ["Skill(pr-workflow:update-pr-description)"]
  }
}

prevent invocation, but the skill's name and description remain in the model's skill listing. That preserves both the context cost and the routing noise.

This matters for users with 100+ installed plugin skills. A plugin may contain valuable workflows alongside one that duplicates a user's existing skill. Today the choices are to carry the duplicate description in every session, fork the plugin, or disable the entire plugin.

Proposed Solution

Allow namespaced plugin keys in skillOverrides:

{
  "skillOverrides": {
    "pr-workflow:update-pr-description": "off",
    "pr-workflow:walk-through-work-history": "user-invocable-only"
  }
}

Expected behavior should match non-plugin skills:

• off: absent from model context and command menus
• user-invocable-only: absent from model context but manually invocable
• name-only: only the namespaced name is listed
• on: current behavior

Verified Behavior

Reproduced on Claude Code 2.1.226:

• Skill(pr-workflow:walk-through-work-history) blocks invocation.
• The denied skill remains visible to the model.
• "pr-workflow:walk-through-work-history": "off" is ignored.
• The skill remains visible and directly invocable.

The current documentation also states that plugin skills are not affected by skillOverrides.

Prior Request

This follows #47747, which covered the same underlying need and was closed automatically as stale. Its closing comment explicitly requested a new issue if the feature remained relevant. The gap remains reproducible in the current release.

Impact

Beyond token cost, large uncurated skill listings reduce skill-selection quality. Duplicate or loosely matching plugin skills compete with the user's preferred workflow even when permission rules prevent the eventual invocation.