I upgraded to the 12.1 version of IDEA from 12.0 and my entire project broke... It will no longer resolve many references within the project - in the same module or otherwise. It seems to be generally related to certain class annotations that it seems to no longer be processing, but I'm not completely sure. Rebuilding doesn't help - in fact, it claims to rebuild fine despite all the errors in shown in the editor. I reinstalled IDEA 12.0 and things work again.