Firmware zip files include batch script. You will also need AVRDude for which I provided link in the “Libraries and Utilities section”.
Latest Firmware (2_04_04) Universal. Compatible w/ V1, please use this one instead of 1.6
Firmware 1.06 (Not recommended. Use V2.02_01 instead.)
You don’t need any of the below if you only want to upload firmware and have no plans to tweak source code. I will attempt to include original source for all the libraries and platforms, however since they were written to work with original Arduino, some were slightly modified (mostly by myself) to work with ATMega644p and ATMega1284p microprocessor.
AVRDude for Windows (if you have Arduino IDE it already comes with AVR inside hardware\etc\ folder)
Hardware Platform Files