It appears that the compilation process is not handling requires in app.js correctly. For example, my app has a requires for Ext.data.* in app.js and I then have a model class that is using a hasMany association (Ext.data.association.HasMany). In this scenario, the resulting ordering is as follows:
My model - 40,763
Ext.define('Ext.data.association.HasMany') - 123,626
Ext.application from app.js - 134,297
If I add a requires for HasMany directly in my model class, then there's no problem.
I am on build 188.8.131.52. I'm not sure whether this is a unique issue or the same as this one: