[BUG] Skills not loading from ~/.claude/skills/ directory

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Skills placed in ~/.claude/skills/ are not being loaded by Claude Code CLI, even after multiple restarts.

Environment:

• Claude Code version: @apple/claude-code: 0.0.124, @anthropic-ai/claude-code: 2.1.5
• Platform: macOS (Darwin 25.4.0)

Steps to Reproduce:

1. Create skill directory: ~/.claude/skills/run-capsule-tests/
2. Add valid skill.json:

{
"name": "run-capsule-tests",
"description": "Trigger Capsule XCTest runs on ATP for Photos UI Automation test suites",
"version": "1.0.0",
"author": "Photos UI Automation Team",
"parameters": [...]
}

1. Add instructions.md with skill instructions
2. Restart Claude Code CLI multiple times

Expected Behavior:

• Skill appears in "Available skills:" section when Claude starts
• Skill can be invoked via /run-capsule-tests command

Actual Behavior:

• "Available skills:" section remains empty
• Skill does not load despite being in correct location with valid configuration
• No error messages displayed

Files:
~/.claude/skills/run-capsule-tests/
├── skill.json
└── instructions.md

Both files are properly formatted and readable.

What Should Happen?

Expected Behavior:

• Skill appears in "Available skills:" section when Claude starts
• Skill can be invoked via /run-capsule-tests command

Error Messages/Logs

Steps to Reproduce

1. Create skill directory: ~/.claude/skills/run-capsule-tests/
2. Add valid skill.json:

{
"name": "run-capsule-tests",
"description": "Trigger Capsule XCTest runs on ATP for Photos UI Automation test suites",
"version": "1.0.0",
"author": "Photos UI Automation Team",
"parameters": [...]
}

1. Add instructions.md with skill instructions
2. Restart Claude Code CLI multiple times

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.5

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Above bug was suggested and all the contents were given by Claude itself