[BUG] Project slash commands in .claude/commands/ not loaded or resolved

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?

Slash commands defined as .md files in .claude/commands/ are not discoverable or executable. They don't appear in autocomplete and don't resolve when typed in full (e.g., /ux-mockup, /commit-all).

The directory contains 28 valid .md command files, all with correct permissions (644) and valid content. Some have YAML frontmatter, some don't — neither type loads.

Plugin-provided skills (e.g from compound-engineering plugin) load and work fine. Only project-level .claude/commands/*.md files are affected.

What Should Happen?

Commands in .claude/commands/*.md should appear in autocomplete and execute
when typed as /command-name.

Error Messages/Logs

Steps to Reproduce

1. Create .claude/commands/ directory in a project
2. Add .md files (e.g., commit-all.md, ux-mockup.md)
3. Start a Claude Code session in the project
4. Type /commit-all or /ux-mockup — command does not resolve
5. Check autocomplete — project commands don't appear

Claude Model

Not sure / Multiple models

Is this a regression?

Yes, this worked in a previous version

Last Working Version

v2.1.87

Claude Code Version

v2.1.89

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

• 28 .md files in .claude/commands/
• Project also uses compound-engineering@scoutworks-marketplace plugin (enabled

in ~/.claude/settings.json)

• Plugin skills load correctly — only project commands fail
• Both .claude/settings.json and .claude/settings.local.json exist — neither

contains strictPluginOnlyCustomization

• No managed settings file present
• File permissions are standard (644), owned by current us