How directly upload arduino generated HEX with avr isp mkii?

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i have atmega 1284p on breadboard , can program atmel studio 6 , avr isp mkii.
the problem prefer use arduino libraries, instead of directly working registers & on.
1. can program & compile arduino & upload generated .hex file using avr isp mkii & atmel studio?
i don't need bootloader @ all, working avr isp mkii , atmel studio easy.
i read instructions here: http://arduino.cc/en/hacking/programmer, , using method error : can not open usb
2. can use header files , libraries of arduino right in atmel studio? if yes, how?
thanks in advance.

you should able program 1284p directly in arduino ide , use "upload using programmer" upload sketches via isp avrispmkii.

1) need have 1284p core arduino ide.
https://github.com/maniacbug/mighty-1284p

2) depending on version avrispmkii programmer have, might able use libusb-filter make available use avrdude , arduino ide.(and still work atmel studio jungo driver)
http://forum.arduino.cc/index.php?topic=160226.msg1202909#msg1202909



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