I suggest you to take as starting point the angular seed project. You could find it on Github.
This project is an application skeleton for a typical AngularJS web app. You can use it to quickly bootstrap your angular webapp projects and dev environment for these projects.
This is the style they suggest to adopt for the controllers.js file:
'use strict';
/* Controllers */
function MyCtrl1() {}
MyCtrl1.$inject = [];
function MyCtrl2() {
}
MyCtrl2.$inject = [];
I also suggest this approach for the development environment. You could compress, and join the files when you will deploy to production.