The problem with all wrappers and extensions is that you're no longer using vanilla Git, which probably breaks other tools like GUI clients. Plus the wrappers a

The problem with all wrappers and extensions is that you're no longer using vanilla Git, which probably breaks other tools like GUI clients. Plus the wrappers and extensions come with their own caveats, so it's still perfectly possible to get the repo into some broken state, only this time your scenario is even more esoteric. I so wish submodules got a better treatment in the vanilla Git.