The dev env unfortunately is such that it creates a duplicate java file in a hidden directory under the same original root for every .java file. This is just a backup mechanism and can't change it. Good thing is this hidden dir name is same. I have Excluded this dir name pattern in the Settings of Intellij IDEA community edition 10.x. Yet, IDE reports this class as a duplicate one. Usages/References as well.
Bonus Q: Is there an eclipse equivalent of Ctrl-O in my IDEA to quickly navigate to methods?