Just one quick question, why not just make the gh-pages branches in your project the main branch instead of master, so it would show that branch right away when you visit you project.
Otherwise, it looks like a great project, and I might use it with my Jekyll blog.
Typically 'master' is where the code is and 'gh-pages' is where the pretty docs are. In your case everything is in gh-pages. Either maintain the code in master and "deploy & display" it on the gh-pages branch or just make gh-pages your master.
come to think of it, that's what i should do with some of my repos ;)