I've just recently come across this project and I'm in the process of changing my dotfiles for use with ghar. I had previously been using Git submodules to include my Vim files etc. I have since got rid of these and will use ghar to add the repos in separately, however I still have many submodules in my .janus file which adds Vim plugins to Janus (https://github.com/carlhuda/janus).

Janus is a very popular project so I would imagine this is quite common although support for Git submodules would be good to have for other uses too. At the moment everything works fine except I have to remember to manually go into the repo and git submodule init && git submodule update before using ghar install to symlink the files.