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I use some 32U4-based PCBs for test fixtures, prototypes, etc. Here's an example project which builds and downloads an example rosserial firmware to a Leonardo board:

https://github.com/mikepurvis/rosserial_leonardo_example

Note that this bypasses the Arduino IDE, assuming that you will use a text editor and catkin_make it from the command line. I also have a more generalized version of this example which I haven't got clearance to release yet—if that's of interest to anyone, let me know and I can move things along with it.