[BUG] ~/.claude/skills/ directory deleted on first run after 2.1.113→2.1.114 update (native binary migration)[BUG]

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?

What's Wrong?

After the auto-update from 2.1.113 to 2.1.114 on April 19, 2026, my entire ~/.claude/skills/ directory was silently deleted on first run. 54 custom skills were lost with no warning and no backup of the file contents.

Timeline:

• Last confirmed skill usage: April 19 at 7:21am (em:sovereign-analysis)
• 2.1.114 binary symlinked: April 19 at 9:10am
• First session after update: skills directory already gone

Evidence:

• ~/.claude/skills/ directory does not exist and has no trace on disk
• Skill names are preserved in ~/.claude/backups/.claude.json under skillUsage (usage metadata only — no content)
• Session logs from April 20 confirm Claude Code itself got "Directory does not exist: /Users/macproajb/.claude/skills" on first run
• No Time Machine, no APFS snapshots — content is unrecoverable

Suspected cause:
The 2.1.113 changelog notes a switch from bundled JavaScript to a native binary. The first-run initialization of the native binary appears to have wiped the skills directory rather than preserving it.

Environment:

• macOS
• Updated from 2.1.113 → 2.1.114
• Install location: ~/.local/share/claude/versions/
• 54 skills lost, months of work, no recovery possible

What Should Happen?

What Should Happen?
The ~/.claude/skills/ directory and all its contents should be preserved across updates, including major runtime changes like the JavaScript-to-native-binary migration introduced in 2.1.113.
At minimum, Claude Code should:

Never delete user-created files in ~/.claude/ during an update or first-run initialization under any circumstances
Back up ~/.claude/skills/ before any migration that touches the config directory, the same way it backs up .claude.json
Warn the user if a migration is about to make destructive changes to their config directory
Include skill file contents (not just usage metadata) in the .claude.json backup so recovery is possible if something goes wrong

Error Messages/Logs

Steps to Reproduce

Note: The deletion appears to happen silently during first-run initialization of the new native binary. No error is shown to the user. The skills simply vanish.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.114 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_