Stefan Penner explains modules well on the Ember App Kit website, but sums it up:
The Ember App Kit uses the ES6 Module Transpiler to convert all your Ember classes to AMD modules. In "normal" Ember development, you assign classes as properties of your application ...
App.IndexController = Ember.Controller.extend(...);
But with EAK, you write your modules in ES6 syntax:
export default Ember.Controller.extend(...);
Transpiler will use the file name as the basis for its module name (provided that it is stored in app/controllers/index.js :
define('controllers/index', Ember.Controller.extend(...));
The Ember App Kit then uses a custom converter to search for modules using AMD, instead of looking for them as properties of your application on camels. (I have no reputation for posting another link, so google for ember-jj-abrams-resolver.)
If Ember searches for a module and does not find it, it behaves the same as outside of EAK.
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