What would be the simplest way to convert an existing application with xib files based on UIWindow into a self contained view controller?
Editing post to address comment from OP:
In future apps, you should avoid acting directly upon a UIWindow whenever possible. However, now that you are stuck with an App A that directly acts upon the window, I would suggest that instead of doing a bunch of work to make your app properly use a UIViewController, you can just make App B into an app that uses two windows:
When App B wants to show the content of App A, just instantiate a new UIWindow windowOfAppA, set its rootViewController to the rootViewController of App A, and then call '[windowOfAppA makeKeyAndVisible];'. Once App A is done doing it's work, it can resign key window status by calling '[windowOfAppB makeKeyAndVisible];'.
Again, I emphasize that the technique I am grudgingly describing is terrible style and in the future your apps should only use one window it should only act upon it when absolutely necessary. Whenever possible, do all your work through view controllers.
Previous content of this answer:
What is your ultimate goal? Are you trying to turn App A into a part of App B? If so, you don't have to make any changes to your existing class hierarchy or nib files. All you have to do is copy all of the files from App A to App B and instantiate App A's root view controller from within App B (perhaps using presentModalViewController:animated:) and everything should work great.