wt-prune

To clean up stale git worktree references, you need to prune the orphaned metadata using git worktree prune. This removes internal references to non-existent worktrees and reports what was cleared, restoring repository consistency without deleting any actual directories.

Git worktree list shows non-existent entries because manual deletion of worktree directories leaves orphaned metadata behind. Pruning these stale git worktree references removes the inconsistent internal listings, ensuring the status output accurately reflects what is actually on disk.

The safest way to prune orphaned git worktree metadata is using git worktree prune, which removes only internal references without touching actual worktree directories. It provides post-clean verification by reporting exactly what was removed and what remains.

To verify repository integrity after pruning stale worktrees, review the post-clean report showing what was removed and what is left. This ensures the remaining git worktree listings are consistent with your disk and no valid references were accidentally lost.

No, git worktree prune does not delete your actual working directories. It safely removes only git's internal stale references and metadata, ensuring non-existent entries are cleared from listings while your valid worktree directories remain completely untouched.

You should run a worktree prune when you notice repository inconsistencies, such as after manual deletions or when worktree listings display non-existent entries. Pruning cleans up the stale metadata and ensures your git worktree status remains accurate.