custom messages under rosjava indigo

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I am working with ros indigo on Xubuntu (Ubuntu 14.04.1 LTS)

I want to create some custom messages for consumption in both Matlab and C++ I'm working on the assumption that in order to do this I need rosjava to generate a jar file from my custom message package.

I've followed the Indigo tutorial for installing rosjava from source. I then started working through the Hydro tutorials only to find that these seem no longer applicable. In the end I simply copied the custom messages package from my catkin_ws/src into my rosjava/src and tried a catkin_make. This seems to have worked but given the complexity of this process under Hydro and can't help feeling I might be missing something.