Yeah, I've used Emacs for Java in the past and the support is not good even if you use JDEE (which is outdated and slow anyhow). I'm an Emacs fanatic, but even so think you would be better off with an IDE in nontrivial Java programs.

I solved the problem by not using Java, but this is obviously not an easy option for you :). Emacs does support Scala fairly well (from what I've heard) with Ensime, for it's worth.