All coding (of AppGameKit stuff) is done in C++. The java is to support it running on Android.
I do my initial coding and testing in Visual Studio, which also provides a very usable debugger.
Once I am content with things working properly, I copy the code files that are NOT AppGameKit specific to the other platform (Xcode and Android) projects and use the appropriate method to build them.
EDIT: My current WIP has 146 .cpp/.h unique files, not including the core AppGameKit ones, between my game app and the level editor. The beauty of Tier 2 is that you can use real OOP and all the great 'native' things like vector, list and string.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master