Ludei, the developers of Cocoon, have put together an official template which takes Andrzej Mazur's Cyber Orb game and adapts it into a Cordova based file structure ready for compiling into a native app.
It also makes use of the Cordova Vibration API. You can clone the template repo and use it directly in the Cocoon cloud compiler, adapting it to your own needs for your own games. This makes the process of working out how best to structure a game for Cocoon native app support a whole lot easier.