I very much prefer this simple method:

https://www.atlassian.com/git/tutorials/dotfiles

tl;dr: it puts the .git directory aside and lets you use it to store any files on your filesystem.

All the usual commands work, except you use something like `config` or `dofiles` instead of `git`:

  $ config add ~/.config
  $ config commit -m initial\ commit

It's pretty much the same as creating a git repository in /, but doesn't mess with your normal git usage (so if you run `git status` in `/home/foo/src/my-awesome-project` and git repository has not been created there yet, git will fail with "not a git repository" and won't show you the contents of your whole filesystem tree).