Plugin skills not discovered when .claude/ directory exists in plugin

Bug Description

When a Claude Code plugin contains a .claude/ directory (for settings, hooks, etc.), the plugin's skills/ root directory is completely ignored during skill discovery. Skills are not loaded with the pluginName:skillName prefix.

Steps to Reproduce

1. Create a plugin with:

• .claude-plugin/plugin.json (standard plugin manifest)
• skills/my-skill/SKILL.md (plugin skills at root)
• .claude/settings.json (project-level settings/hooks)

1. Install the plugin: claude plugin install <plugin>

1. Run /reload-plugins — skills from skills/ are not loaded

1. Remove .claude/ directory from the plugin cache

1. Run /reload-plugins — skills from skills/ are now loaded with pluginName: prefix

Expected Behavior

Plugin skills in skills/ should be discovered regardless of whether .claude/ directory exists. The .claude/ directory is used for settings/hooks and should coexist with plugin skills.

Actual Behavior

When .claude/ directory is present in a plugin, the skills/ root directory is ignored. Only .claude/skills/ is searched for skills (if it exists).

Evidence

Tested with 5 plugins on Claude Code v2.1.92:

| Plugin | .claude/ dir | Skills loaded? |
|--------|---------------|---------------|
| oh-my-claudecode (4.10.2) | ❌ absent | ✅ Yes |
| my-skills (1.3.0) | ❌ absent | ✅ Yes |
| scheduler (0.2.0) | ❌ absent | ✅ Yes |
| codex (1.0.2) | ❌ absent | ✅ Yes |
| laplace-dev-hub (1.9.0) | ✅ present | ❌ No |

All plugins use the same skills/<name>/SKILL.md structure with identical frontmatter format.

What I've tried (none worked)

1. Adding "skills": "./skills/" to .claude-plugin/plugin.json
2. Removing .claude/skills/ subdirectory while keeping .claude/
3. Creating symlink .claude/skills -> ../skills

Workaround

None found. The .claude/ directory contains essential settings and hooks that cannot be removed.

Timeline

• Skills worked when plugin only had skills/ (no .claude/ dir) — Feb 13, 2026
• Skills stopped working after .claude/ directory was added — ~Feb 25, 2026

Environment

• Claude Code: v2.1.92
• macOS Darwin 25.2.0
• Plugin installed via marketplace (scope: user)