Submodule and worktree checkouts store .git as a file (gitdir: pointer);
the carry-over only looked at directory names, so that form was still lost
on rollback. Handle files with the same guard. Docstring now states the
deliberate limit: an excluded entry whose skill dir the target snapshot
lacks is dropped with staging (no orphan .git) and is not undoable via the
safety snapshot, which excludes these paths as well.
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