[BUG]

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?

Body:
## Description
Custom commands in .claude/commands/ are not recognized after upgrading to v2.1.89.
Typing /pulse returns "Unknown skill: pulse". Commands worked in previous versions.

## Steps to Reproduce

1. Have custom command files in .claude/commands/ (project-level)
2. Upgrade to v2.1.89
3. Type /pulse (or any custom command name)
4. Get "Unknown skill: pulse" error

What Should Happen?

## Expected
Custom commands should appear in autocomplete and execute when invoked.

Error Messages/Logs

Steps to Reproduce

i don't lknow how to fix this

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

v2.1.89

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Warp

Additional Information

_No response_