Please look at native extensions:
Really you do not need most staff created in new extension by generator. What you need is just integrated build support for additional java files.
In case you want to call plugin relates java directly you may face java classpath problems. It depends on extensions build sequennce...
In case the problem will occur please contact me directly by email: email@example.com
Thanks for the help. We are still facing the issue though with the build. It appears our libraries are not loaded in the build command that gets generated. Are there any examples of how this would work with sample projects (and third party binaries)?