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
I recently encountered this same problem on a project using the AppGyver Supersonic framework and a Heroku app.
Our Supersonic app lived in root so it wasn't an option to have Heroku living there too. In the end we moved our Heroku app to a subdirectory named web/. We now deploy to Heroku using:
git subtree push --prefix web heroku master