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git worktree prune removes the metadata directory as a whole, but the agent sandbox pins config.worktree and commondir as read-only bind mounts, so the unlink fails with EBUSY and the stale entry keeps claiming its branch. Dropping gitdir and HEAD unregisters it without needing the pinned files gone.
System Scripts
This directory holds system-facing helpers grouped by area. Use the README in each child directory as the canonical entry point for that area. For the canonical Make target index that invokes these helpers, see make.md.