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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?

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    Please don't ask two questions in one. It's convenient for you but makes your question less useful to others looking for the same things in the future. Commented Jan 10, 2013 at 18:13

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How exactly did you exclude it? It should be added to the list of ignored folders in Settings | File Types. If it doesn't work, file a bug.

Bonus Q: Is there an eclipse equivalent of Ctrl-O in my IDEA to quickly navigate to methods?

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