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If you are implementing your own main(), I recommend looking at the rosjava_bootstrap run.py script and adapting it to your own needs. The main thing of note is the Python routines for constructing the classpath.

Also of note is the RosRun.java, which shows the basic bootstrapping steps that you'll need for constructing a context.

All of this will get better over time -- we are evolving the toolchain to try and find the sweet spot of compatibility with the many different and varied frameworks that Java provides (e.g. Eclipse, ant, Maven, OSGI, Android, etc...).