1) Flash FC firmware:
# reset running firmware (MCU will execute bootloader only for ~1s!)
$ echo -e -n "#aR@S\r" > /dev/ttyUSB1

# flash new firmware
$ avrdude -p m644p -c butterfly -b 57600 -P /dev/ttyUSB1 -U flash:w:/tmp/Flight-Ctrl_MEGA644_V0_82a.hex


2) Flash BLMC firmware (via twiboot):
# enter bootloader (0x1B, 'S'), select first twi-slave ('1'):
$ echo -e -n "\x1BS1" > /dev/ttyUSB1

# flash new firmware
$ avrdude -p m8 -c butterfly -b 57600 -P /dev/ttyUSB1 -U flash:w:/tmp/blmc.hex

# select next twi-slave (bootloader is still active)
$ echo -e -n "2" > /dev/ttyUSB1


3) Other Commands:
'0'       => select FC internal flash/eeprom
'1' - '4' => select twi-slave 1-4, print bootloader version
'I'       => start application on selected twi-slave, print application version
'l'       => start selected motor
'k'       => stop selected motor