Update initializer to be an instance initializer

[jnhuynh]

Ember has deprecated accessing the container instance insider of initializers. Instead there is this notion of instanceInitializers. We should update to mirror that.

We will need to update setup.js to work different or break it up into two separate methods. One that gets called by an initializer that has access to the registry and application and another to be called by instanceInitialzier that has access to the instance.container.

[jcope2013]

#517
#564
#560

[jnhuynh]

Sorry about that, should have checked more thoroughly.