Duy Nguyen [off-list ref] writes:
No, the point is people make mistakes. What do we do in that case? Or
will you introduce yet another "gc" command for clean up ~/bare?
I do not know if it will be a "gc", but we would need a way for the
user to say "I no longer need the repository for this submodule kept
locally here (I may have to re-clone when I check out a version that
needs the submodule)" to free up the .git/modules/<name> directories
in the superproject. We might want to allow "submodule deinit" to
also ask for it, but "deinit" will not be the only occasion the user
might want it.
It is already a problem that needs to be addressed in the current setup.