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submodule.move seems to get me half the way there, but it misses a couple things. In new versions of git the .git is just a textfile that references a path in the base directory. This file isn't updated if you move directory depths because it is relative.
It also doesn't update the submodule name in the .git/config which would be helpful. I'll probably be writing the code to do this, but documentation on submodule.move would help too.