Previously, I detailed how I was using git submodules and gh-pages at github to host the html versions of my documentation generated by sphinx. Basically, the problem is that using git submodules for this is a real pain (for me, at least). You've always got to remember to sync up the submodule(s) just so, or things go horribly wrong and stop tracking each other.

Because I can never remember the correct order of what needs to be committed when, I searched for other ways. And searched. And searched. Finally, I ginned up something that I think I like. It basically uses a directory, within your project but ignored by .gitignore, to keep track of your gh-pages content. Because the .git directory tracks what you need to track, you can run make html for sphinx with impunity, and you can push your changes to gh-pages when you want - no need to remember what goes when and where.

Finally, you can track the raw rst of your doc files in the regular source tree, just like you should.