First, here are the docs on what the GUI does: http://www.arduino.cc/en/Hacking/BuildProcess http://www.arduino.cc/en/Hacking/BuildProcess That alone should b

First, here are the docs on what the GUI does: http://www.arduino.cc/en/Hacking/BuildProcess http://www.arduino.cc/en/Hacking/BuildProcess That alone should be enough to get you going -- it's a pretty straightforward compile+link+upload process, with only a funky preprocessor that makes their language easier to deal with than C or C++ for beginners (doesn't require includes or care about order of function declaration | prototyes ).