I'm switching from submodules to subtrees. To do this, I've created a topic branch and done the work in there. To get everything working properly, I had to delete the submodule folders entirely from disk. Once I have the subtrees set up in my branch, I can't checkout to move back and forth between my topic branch and the master branch because once I have the submodule re-established, they end up leaving their files as untracked files when trying to switch back to my subtree branch and I have to go and clean them up off of disk again. I'm wondering if this is a known issue and if there's any plans to do anything about it.