[BUG] Skills/commands appear duplicated when using git worktrees

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?

Description

When running Claude Code inside a git worktree, skills defined in
.claude/commands/ appear twice in the /skills list. Claude Code
loads commands from both the current worktree directory and the main
worktree directory, causing duplicates.

Expected Behavior

Each skill/command should appear once in the list.

Actual Behavior

Commands from .claude/commands/ appear twice — once loaded from
the main worktree's .claude/commands/ and once from the current
worktree's .claude/commands/.

Example duplicate entries in the system prompt:

- chlog: Update the docs/changelog.md file based on changes in the current branch.
- commit: Create a git commit for the current changes following project conventions.
- pr-review: Review the current branch changes based on the mpl2 Pull Request Checklist.
- rebase-main: Fetch the latest changes from origin and rebase the current branch from main.
- chlog: Update the docs/changelog.md file based on changes in the current branch.
- commit: Create a git commit for the current changes following project conventions.
- pr-review: Review the current branch changes based on the mpl2 Pull Request Checklist.
- rebase-main: Fetch the latest changes from origin and rebase the current branch from main.

Environment

• Claude Code CLI
• Windows 11, bash shell
• Git worktrees created via git worktree add

Suggested fix

Deduplicate skills by name when loading from multiple .claude/
directories (e.g., prefer the current worktree's version, or
deduplicate by command name).

What Should Happen?

Each skill/command should appear once in the list.

Error Messages/Logs

Steps to Reproduce

1. Have a git repository with .claude/commands/ containing command

files (e.g., commit.md, chlog.md)

1. Create a git worktree: git worktree add ../my-worktree feature-branch
2. Open Claude Code in the worktree directory
3. Run /skills

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.49

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_