[FEATURE] Let `skillOverrides` disable individual plugin skills

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

skillOverrides has no effect on skills that come from a plugin. The only way to drop an unwanted plugin skill is to disable the whole plugin, which also drops its MCP servers, hooks, and the skills you do want.

This was requested in #47747, which the stale bot closed with a note to open a new issue if it's still relevant. It still is on 2.1.282.

Concretely, the official aws-core plugin ships 19 skills plus the aws-mcp documentation server and a secret-safety.py PreToolUse hook. I want the docs server, the hook, and aws-core:aws-cdk. The other 18 skills (Bedrock, Swift SDK, containers, billing, and so on) are irrelevant to my work, but they stay in the model's skill listing and in the / menu.

Setting this in ~/.claude/settings.json does nothing:

{
  "skillOverrides": {
    "aws-core:amazon-bedrock": "off",
    "aws-core:aws-sdk-swift-usage": "off"
  }
}

The override is ignored silently. The only hint is the "A plugin skill is managed with the plugin, not here." message when you try to toggle one from /skills. As far as I can tell, override resolution locks every plugin skill to on (source plugin) before it reads any settings.

Proposed Solution

Let skillOverrides apply to plugin skills, keyed by their namespaced name (plugin:skill), with the same on / name-only / user-invocable-only / off values that already work for user and bundled skills. The plugin stays enabled, so its MCP servers, hooks, and remaining skills keep working.

Keying by name means an override survives plugin version upgrades. A skill added in a later plugin release stays on until the user opts it out.

Alternative Solutions

Today the workaround is to disable the plugin, re-add its MCP server by hand with claude mcp add, copy its hook into settings.json, and vendor the one skill you want. That loses plugin updates for all three.

Codex CLI already handles this for the same aws-core plugin:

[plugins."aws-core@agent-toolkit-for-aws"]
enabled = true

[[skills.config]]
name = "aws-core:amazon-bedrock"
enabled = false

Priority

Medium - Would be very helpful

Feature Category

Configuration and settings

Use Case Example

1. Enable a broad first-party plugin such as aws-core for its MCP server.
2. Set "aws-core:<skill>": "off" in skillOverrides for each skill that isn't relevant.
3. Those skills disappear from the model's listing and the / menu, while the plugin's MCP server, hooks, and remaining skills keep working.

Additional Context

Claude Code 2.1.282, Linux (WSL2).