One thing I’ve been thinking about is that it would be nice to tag files with the program that created them. Aside from the clutter in my home directory, I have a lot of files that I have to guess as to where they originated from based on metadata like modification timestamps or permissions, but it would be nice to see something like “~/.config was created by some-tool”.
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.