.claude/commands/ files deleted within seconds of session start (v2.1.81)

Description

Files in .claude/commands/ are deleted within seconds of a Claude Code session starting. The files exist on disk before launch, are briefly visible in the session (slash commands appear momentarily), then vanish. After deletion, /skills shows no user commands.

Environment

• Claude Code v2.1.81
• Windows 11 (MSYS2/Git Bash)
• 76 .md files in .claude/commands/

Reproduction

1. Verify files exist: ls .claude/commands/ | wc -l → 76
2. Launch claude in the project directory
3. Skills appear briefly in the session
4. Within seconds, skills disappear
5. From another terminal: ls .claude/commands/ | wc -l → 0

Files persist indefinitely when Claude is not running. Deletion only occurs during active sessions.

Hooks disabled

Both PreToolUse hooks were disabled (replaced with no-op echo commands in global settings) — files still vanish. This rules out hook scripts as the cause.

Related

• #34330: .claude/skills/ deletion bug (v2.1.76+) — same behavior but for skills directory
• Our files are in .claude/commands/ not .claude/skills/, but the behavior is identical

Impact

This affects a shared skills library that serves 20+ projects via symlink junctions. When the source files vanish, every project loses all slash commands and hooks simultaneously.