This bootloader is a modified CDC bootloader from LUFA using the avr109 protocol.
Example command to flash with the FTDI TUMPA device:
$ avrdude -c tumpa -p m16u2 -v -e -u -U flash:w:BootloaderCDC.hex -U lfuse:w:0xDE:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0xCF:m