[warfangle]

There's the official arduino command line tool: https://github.com/arduino/Arduino/blob/ide-1.5.x/build/shar...

But you need to use their (terrible) IDE for writing your sketches this way.

You can also use avr dude; there's a sample makefile available here: http://playground.arduino.cc/Learning/CommandLine#.UzQ_ca1kF...