Using inotools to upload to Arduino

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My robot project uses a headless Ubuntu install for ROS, with a networked Ubuntu VM for doing GUI ROS tasks, and I'd like to be able to edit and upload Arduino firmware from SSH directly.

I managed to get ino installed to do Arduino compiling but it stalls repeatedly because it can't find ros.h. Has anyone successfully uploaded rosserial firmware with ino or any other command line utility? I've coped the ros_libs folder into the ino workspace lib folder but that doesn't help.