Protected paths are directories Claude Code refuses to modify without explicit, targeted approval - even in bypass mode.

What it does

.git, .claude, .vscode, and similar metadata directories are guarded by default. Edits or writes to anything inside them require a specific permission grant, not a blanket allow. It's a structural safety net - you can't accidentally rewrite your git history or clobber your Claude config by running a wide prompt.

When to use it

Always. Protected paths are on by default and you should leave them on.
Add your own sensitive paths to the guard list for project-specific safety.
Pair with audit logging to catch attempts even when denied.
Keep the guard in place even for trusted agents - the defense layers compound.

Gotchas

Some legitimate workflows need to touch .git (tools that rewrite hooks, for example). Grant tightly scoped rules for those.
Protected paths don't prevent reads. Claude can still see what's there.
Custom protected paths live in settings. Changes apply on session restart.

Official docs: https://code.claude.com/docs/en/permission-modes.md#protected-paths