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In case anyone ever has the same problem and finds this thread:

Adding it to the catkin workspace is not necessary. I opted to use a modified version of the rosjava build script (located at project/build/install/project/bin/project). as this seemed the best way to run org.ros.RosRun which has to call onStart. The class the code from the question is in is passed as an argument to RosRun/the build script.