The ATmega8U2 firmware source code is available . The ATmega8U2 is loaded with a DFU bootloader, which can be activated by connecting the solder jumper on the back of the board and then resetting the 8U2. You can then use Atmel's FLIP software (Windows) or the DFU programmer (Mac OS X and Linux) to load a new firmware. Or you can use the ISP header with an external programmer (overwriting the DFU bootloader). See this user-contributed tutorial for more information.
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