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I think the (2) is appended to the bot name because it was a battle with two of the same bot. But I don't understand how RoboResearch could have gotten confused enough for that to happen. I think Skilgannon is right that it's confusing the parsing going on in BattleResults.load, though I can't exactly follow how (because I'm not too familiar with the format of the output it parses).
I'd really like to modify RoboResearch to use the Robocode control API, or write a new batch battle runner that does. RoboResearch runs a battle in a fresh Robocode instance each time from a .battle file and parses the results from the output. I recently tinkered with this - starting a new JVM each time is a lot more painful when you're running 1-round battles, like I was for my perceptual gun =). And I realized it requires a separate Robocode install for each thread, or you hit concurrency exceptions reading in JARs. RoboResearch makes use of a debug property that starts Robocode with a different "working directory" so each thread can load bots from a different directory, but there's really no way to do that for separate threads using the Robocode control API. (Not that it's a big deal to have a bunch of full Robocode installs, but it would make the change to RoboResearch quite a bit more complicated.) Also, the SQL db it uses slows down a lot once you have a lot of results in there, forcing me to manually clear it from time to time. I'm sure there's a better solution.