The Makerbot usbserial 8U2 firmware is based on Arduino's 8U2 usbserial firmware.  Thanks Arduino! (www.arduino.cc)
...And that firmware is based on LUFA (See the LUFA/readme.txt and LUFA/License.txt file).

The Makerbot 8U2 Source Code can be found in the src/Projects/makerbot directory

*Note, a .inf Driver file is required to use the MightyBoard with windows.  It can be found in the ReplicatorG drivers folder.

TO DOWNLOAD THE HEX FILE:
1. Connect the AVR ISP MKII compatible programmer to the 8U2 6 pin programming header
2. Ensure the Board is Powered
3. navigate to the directory containing the .hex file in the terminal
4. Execute the following avrdude command: avrdude -p at90usb82 -F -P usb -c avrispmkii -U flash:w:Makerbot-usbserial.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
5. If unsuccessful ("Error in USB Receive"), try again.  It sometimes takes a few tries

IF YOU NEED TO RECOMPILE THE HEX FILE:
*This is only necessary if you have made changes to the 8U2 Source Code
*This works with avr-gcc v4.3.3 on Mac osx.  It does not work with avr-gcc v4.5.3 on ubuntu. Testing with alternate gcc versions has not been done
1. Enter the makerbot project directory in the terminal
2. Run "make clean"
3. Run "make"
4. Your hex file will be generated in the currect directory