[bradyd]

I haven't personally done this yet, so I'm not sure if there is more to it, but there is a program called AVRDUDE[1], used to load the firmware onto the boards. I know that the Arduino IDE uses this behind the scenes. I'm not really sure about the compilers involved. Basically the Ardunio environment is just the toolchain and a bootloader. I know that there are a few different bootloaders around for the Adrduino compatible chips (such as the Adafruit "No-wait" bootloader[2]) to look for inspiration.

[1] http://www.nongnu.org/avrdude/ [2] http://learn.adafruit.com/arduino-tips-tricks-and-techniques...

[Thrymr]

The compiler is just avr-gcc, you can use that and upload code with avrdude directly, bypassing (or even overwriting) the bootloader. You don't even need an Arduino, with the right breakout board and serial connection you can write directly to a naked microcontroller.