Agent destroyed uncommitted work by copying worktree files over working directory

Bug Report

What happened:
Claude Code agent launched worktree-based sub-agents that started from git HEAD (clean state), missing all of the user's uncommitted changes. The agents then force-copied their output files back into the user's working directory, overwriting days of uncommitted work across multiple files.

Files destroyed:

• server/routes/bookings.js (pro pay assignment changes)
• web/src/app/[orgSlug]/book/page.tsx (Stripe Connect fix, Nominatim proxy, spec UX redesign)
• mobile/apps/field-pro/app/(tabs)/jobs.tsx
• mobile/apps/field-pro/app/(tabs)/more.tsx (language picker)
• web/src/app/(dashboard)/layout.tsx

Impact:

• Multiple days of development work were overwritten
• No git commits existed to recover from (changes were unstaged)
• VS Code local history was empty — no recovery path
• User had to wait while recovery agents attempted to reconstruct lost work from conversation transcripts

Expected behavior:

• Worktree agents should NEVER copy files back over the user's working directory without explicit permission
• If the working directory has uncommitted changes to files the agent wants to modify, the agent should warn the user and ask before proceeding
• Uncommitted work must be treated as sacred — it represents in-progress work that may not exist anywhere else

Severity: Critical — data loss of user's work product

Environment: Claude Code CLI, macOS, git repo with uncommitted changes