how to flash atmega16u2 for a arduinoDUE based project

aureliusss:
hello everyone,
i'm working on project based on Arduino DUE. i've already printed my pcb and now i need to flash the atmega16u2.
according to this guide http://arduino.cc/en/Hacking/Upgrading16U2Due i shouldd be able to flash it siply connecting to the usb and then execute avrdude.exe from the cmd program(i'm using windows seven), but in my arduino due IDE (1.5.2) i can't find avrdude.conf nor the hex file.
where can i find them?

No, according to that article you need to flash a special sketch to an Uno or Mega and use it as an ISP (or use a normal ISP tool) to connect to a six pin connector on the Due that lets you flash the 16U2 chip. You can't just program that chip through the USB port.