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Use the programmer, found in the box of 'usbtinyisp'. Connect it with the 6-pin header to the ICSP on the Arduino (Tested with Nano)

Writing a bootloader to an 'empty' Arduino or atmega:

avrdude -p m328p -c usbasp -B 4 -U hfuse:w:0xda:m -U lfuse:w:0xff:m -U efuse:w:0x00:m avrdude -p m328p -c usbasp -U flash:w:~/arduino/bootloaders/atmega/ATmegaBOOT_168_atmega328.hex -U lock:w:0x0f:m