deprecate Ember.Application#initialize

This was never intending to be supported. It was
used to deal with app initialization shortcomings.
Hopefully all of those have now been dealt with.

In situations where default initialization behaviour
is not wanted please use Ember.Application#deferReadiness
and Ember.Application#advanceReadiness.
Merge pull request #2364 from stefanpenner/deprecatedAppInitialize

deprecate Ember.Application#initialize