I have one \'super\' repository in GitHub which will contain several applications I would like to deploy to Heroku. Here is an example of my repository.
/app
What do you think about creating a local git repository in /app/website, and using Git Hooks so that when you commit, it'll commit your website code as well?
The basic answer, from my perspective, is that you'll want a git repository at the website level, not a parent level. Everything from there depends on your point of view -- do you wan the /website to be its own repository with /app using a submodule for /website? (That's the way I'd go)