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I got Visual VM working and running through Eclipse too. Its a bit unintuitive to set up through Eclipse but its working now and easy to run. As MN says you can filter out any results from specific packages and just profile your bot (though its worth noting that you might want to leave any java data structure packages such as the Vector class if you use it a lot in your robot).

I managed to get my movement running pretty fast within an hour of getting Visual VM running! :D

If I find the time I might write a wiki page on how to get it up and running in Eclipse and how to set it up to profile your robot.