[FEATURE] Add project-level configuration to enable/disable specific 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

Currently, all skills in ~/.claude/skills (user-level) are automatically loaded for every project. There is no way to
selectively enable or disable specific skills at the project level through .claude/settings.json.

This becomes problematic when:

• Users have many skills installed globally but only want a subset available for specific projects
• Different projects require different workflows (e.g., TDD workflow vs. planning-focused workflow)
• Teams want to enforce specific skill usage patterns for certain projects

Current Workaround Limitations

The only current workaround is to create project-level skills in .claude/skills/ with symlinks, but this:

• Requires manual setup for each project
• Doesn't actually disable user-level skills (both appear in the skill list)
• Is cumbersome to maintain

Proposed Solution

Add a configuration option in .claude/settings.json to control skill availability at the project level.

Option 1: Whitelist approach
{
"enabledSkills": [
"skill-a",
"skill-b",
"skill-c"
]
}

Option 2: Blacklist approach
{
"disabledSkills": [
"skill-d",
"skill-e",
"skill-f"
]
}

Option 3: Combined approach (most flexible)
{
"skills": {
"mode": "whitelist", // or "blacklist"
"list": ["skill-a", "skill-b", "skill-c"]
}
}

Expected Behavior

When configured in project settings:

• Only enabled skills appear in /skills list
• Only enabled skills can be invoked
• User-level skills remain unchanged for other projects
• Configuration is simple and declarative

Use Case

A user wants to use a specific workflow for a project, enabling only 3 out of 19+ globally installed skills (skill-a,
skill-b, skill-c), while keeping all skills available globally for other projects.

Alternative Solutions

_No response_

Priority

Medium - Would be very helpful

Feature Category

Configuration and settings

Use Case Example

_No response_

Additional Context

_No response_