If someone is still looking for the answer. I encountered the same problem as the one described above.
I have the ember application installed by yeoman. It provides an app.js file:
var TodomvcEmber = window.TodomvcEmber = Ember.Application.create();
/* Order and include as you please. */
require('scripts/controllers/*');
require('scripts/store');
require('scripts/models/*');
require('scripts/routes/*');
require('scripts/views/*');
require('scripts/router');
noticed that in my .tmp/scripts/combined-scripts.js file the added controllers I had put in /scripts/controllers/todos_controller.js, wheren't integrated. In the app.js file, I changed the order of the require ( put the require of the controller a bit downwards )
var TodomvcEmber = window.TodomvcEmber = Ember.Application.create();
/* Order and include as you please. */
require('scripts/store');
require('scripts/models/*');
require('scripts/controllers/*');
require('scripts/routes/*');
require('scripts/views/*');
require('scripts/router');
And that did the trick for me.