Project-level skills in git worktrees not discovered since 2.1.104

Description

Project-level skills defined in .claude/skills/ within a git worktree are no longer discovered as of version 2.1.104. The skill file exists and has valid frontmatter, but /skill-name returns "Unknown skill."

Repro

1. Have a git repo with a worktree: git worktree add .worktrees/mybranch
2. In the worktree, create .claude/skills/my-skill/SKILL.md with valid frontmatter
3. Launch Claude Code from the worktree directory
4. Run /my-skill → "Unknown skill: my-skill"

Expected

Skills in the worktree's .claude/skills/ should be discovered, same as the main repo's .claude/skills/.

Observed

Only skills in the main repo's .claude/skills/ (resolved via git rev-parse --git-common-dir) are discovered. The worktree's .claude/skills/ is ignored.

Note: CLAUDE.md in the worktree IS read correctly — only skill discovery appears affected.

Environment

• Claude Code 2.1.104 (macOS, Darwin 24.6.0)
• Worked correctly on 2.1.100 and 2.1.101
• Broke after auto-update to 2.1.104 on April 12, 2026

Workaround

Symlink the skill directory into the main repo's .claude/skills/.