- Make changes to firmware in Arduino software.
- Save as hex
- sftp/scp the file to the Raspberry Pi
The last step was the one that gave me so much grief. For my particular setup, here's the command that works:
avrdude -p m2560 -c stk500v2 -P /dev/ttyUSB0 -D -U flash:w:Marlin.ino.mega.hex:i