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The class BuidlConfig in ajdt.core seems to have a very inefficient way of constructing the list of included source files. Also, why are the source files returned as a list, wouldn't a set be better? I notice that the AJBuilder is traversing this list multiple times. This list could potentially be large (includes every single source file in the project). I don't know what kind of performance impact this actually has, and I should test it out before doing any premature optimizations.
After doing a little bit of testing on my own, it seems that this is not a big problem. I tested on a medium sized project (ajdt.core itself) by timing the loop that creates the included source files list as well as traverses it multiple times. The result is 3 miliseconds spent doing it. So, this is not worth my time to optimize.