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how do i change which tree its using

You'll need to extract the .jar file, and make a new wrapper class in net/robowiki/knn/implementations directory, similar to the other ones there. Then at the top of net/robowiki/knn/implementations/KNNBenchmark.java you'll need to add a reference to the tree you want to test, like the others are referenced.

how do i make a new knn.jar with the latest skilgannon kd-tree

You don't need to. Just run the KNNBenchmark by java KNNBenchmark.class

it doesn't work

on my ubuntu i only have icedtea and openjdk