Auto-update removes user symlinks from ~/.claude/skills/

Bug

Claude Code auto-updates silently remove symlinked skill directories from ~/.claude/skills/. Real directories in the same location survive updates, but symlinks are lost.

Reproduction

1. Create a custom skill in a separate repo/directory (e.g. ~/code/claude-skills/coding-rich/SKILL.md)
2. Symlink it into the skills directory:

``bash
ln -s ~/code/claude-skills/coding-rich ~/.claude/skills/coding-rich
``

1. Verify the skill loads in Claude Code sessions — works correctly
2. Wait for Claude Code to auto-update (daily)
3. After the update, ~/.claude/skills/coding-rich symlink is gone

Evidence

• ~/.claude/skills/qwen-draft/ (real directory) — survived months of updates
• ~/.claude/skills/coding-rich (symlink → ~/code/claude-skills/coding-rich) — removed at some point during updates
• Both were created at the same time (April 9, 2026) and the symlink worked for weeks before silently disappearing

Expected behavior

User-created symlinks in ~/.claude/skills/ should be preserved across auto-updates, just like real directories are.

Impact

Custom skills with description: "Apply this skill for ALL coding tasks" silently stop loading. There's no warning or error — the skill just disappears from the available-skills list. The user has no way to know it's broken until they notice degraded output quality.

Environment

• macOS (Apple Silicon)
• Claude Code (latest, auto-updating daily)
• Skills directory: ~/.claude/skills/