My .vim repository used to track bundle/Vundle.vim as a Git submodule.

But I found it was no longer necessary so I removed the Git submodule:

git rm bundle/Vundle.vim
rm -rf .git/modules/bundle/Vundle.vim
rm .gitmodules

Stackoverflow mentioned using git submodule deinit:

git submodule deinit -f bundle/Vundle.vim

But I didn’t have to use it.