[BUG] ~/.claude/skills/ completely ignored since 2.1.186 (regression)

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?

Version: 2.1.190 (native, darwin-arm64)
▎ Regression introduced: between 2.1.179 (working) and 2.1.186 (broken)
▎ /reload-skills returns exactly 13 skills (built-in only) regardless of:
▎ - flat .md files in ~/.claude/skills/
▎ - directory/SKILL.md format in ~/.claude/skills/
▎ - running with --safe-mode
▎
▎ Rolling back to 2.1.179 via npm restores 91 skills correctly.

What Should Happen?

Custom skills defined in ~/.claude/skills/ (both flat .md and directory/SKILL.md formats) should be discovered and loaded by /reload-skills, appearing alongside built-in skills in the skill list — consistent with behavior in 2.1.179 and earlier.

Error Messages/Logs

When running /skills, claude returns: No skills found

Steps to Reproduce

For my setup:

1. Install Claude Code via the native installer (darwin-arm64), auto-update channel: latest
2. Create one or more skills in ~/.claude/skills/ — either flat (~/.claude/skills/my-skill.md) or directory format (~/.claude/skills/my-skill/SKILL.md) with valid frontmatter:

---
name: my-skill
description: Test skill
---

1. Open Claude Code and run /reload-skills
2. Observe: only 13 built-in skills listed — custom skills in ~/.claude/skills/ are absent

Expected: custom skills appear in the list
Actual: only 13 built-in harness skills listed regardless of what is in ~/.claude/skills/
Additional negative findings:

• Reproduces with claude --safe-mode (rules out plugin interference)
• Reproduces with both flat .md files and directory/SKILL.md format
• /doctor reports no issues

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.179

Claude Code Version

2.1.190

Platform

Other

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_