Yeah, in some way it's something the VCS are lacking right now: being able to add files outside the .git/ parent directory, so you can index a given directory i

Yeah, in some way it's something the VCS are lacking right now: being able to add files outside the .git/ parent directory, so you can index a given directory in multiple working trees/repositories. So you can have a ~/dotfiles working tree that points to ~. And perhaps a ~/mydata working tree that points to ~ as well. Both will index different files as manually added by the user.