When I do atmega328 on arduino uno,i do the bootloader through Atmel studio 7.0 and AVRISP mkII
It it possible to do the bootloader for arduino yun atmega32U4 through Atmel studio 7.0 and AVRISP mkII?
Yun has application and bootloader firmware source code build in.
/usr/bin/run-avrdude /etc/arduino/Caterina-Yun.hex
http://forum.arduino.cc/index.php?topic=209587.msg1542895#msg1542895