When you call Ext.regApplication is creates a namespace for your application, and the sub-namespaces:
application.models
application.views
application.controllers
application.stores
You can see this in src/Application.js
I've been laying out my code in the same way, in-line with how you generally layout namespaces in another language on disk (i.e. .NET).
I have a few applications spread across repos, and seems to work well. The main application entry point sorts the viewport out, with the other application launch methods wiring up Direct providers and stuff as needed.
Is it possible to create another folder-structure for Extjs4 MVC-application with modules, because if application's controllers count is too large, it will be a headache to write another mvc-component and maintain all my code. In my test-application I cannot create module-structure, because of Ext.Loader. What is the best solution for this?