Re: your edit, Yeah it can! Set up a folder, say 'vim' for your example, and then inside of that folder you have a '.vim' file and a '.config/nvim' file.
Then when you run `stow vim` from the parent of the original 'vim' folder it will symlink everything in there to ~.
You can even have more folders that have a '.config/foobar' inside of them, and when you stow those it will all work itself out nicely!
Edit: You can find examples of this in my dotfiles https://github.com/AnthonyWharton/dotfiles/ (I use stow if you didn't guess :P). For example look at the 'i3' folder and the 'polybar' folder, they both add things to '~/.config '
Then when you run `stow vim` from the parent of the original 'vim' folder it will symlink everything in there to ~.
You can even have more folders that have a '.config/foobar' inside of them, and when you stow those it will all work itself out nicely!
Edit: You can find examples of this in my dotfiles https://github.com/AnthonyWharton/dotfiles/ (I use stow if you didn't guess :P). For example look at the 'i3' folder and the 'polybar' folder, they both add things to '~/.config '