Per conversation with @bpinto in Gitter.
There's no need for two separate directories. You don't have a `.git` and `.git-custom` folder, you just put your config in `.git` :)
The most straightforward interpretation of XDG basedir spec is that user configuration for omf would go in `~/.config/omf`, so let's put it there. The only question is whether omf-generated config (i.e. the `theme` file) should go there as well. By analogy with git, programmatically generated config should probably be merged in with user config. This also makes it so when a user clones their dotfiles to a new machine, both kinds of settings come with it.
Justin Hileman
Bruno
Jorge Bucaran