i was busy with my app for over a week, when suddenly:
11-12 07:59:17.860 1653-1653/nl.test.myapp E/AndroidRuntime﹕ FATAL EXCEPTION: main
java.lang.Runtim
I had the similar problem. I remembered, that previously "not enough memory" message was shown and the application uploading process could not finish, stopping on dexDebug with error. Then I released enough memory, but application started with ClassNotFoundException.
The solution that worked for me was to delete all "build" folders in the project. I suppose that gradle can put corrupted files to "build" folder when there is not enough memory.