not sure if this is the exact solution to your problem, but rcm (https://github.com/thoughtbot/rcm) allows you to create dedicated dotfiles in a .dotfiles directory which are being symlinked back to files, and it has a -t option to create and restore dotfiles with tags. mkrc -t emacs .emacs.d would create a .dotfiles/tag-emacs/ folder and rcup -t emacs restores it.