Bootloader is to make firmware upgrade over the serial/USB possible.
Bootloader is always programmed and should not be programmed unless 
you screwed it up. It should be programmed w. an ISP-programmer and 
proper fuses for the AVR should be set. If hacking you should know 
this.

The new bootloader fixes a wdt_reset problem for atmega128rfa1.

# Programming the bootloader:
avrdude  -p atmega128rfa1 -c jtag2isp   -P usb -e -U flash:w:main.hex

# Programming the fuse bits:
avrdude  -p atmega128rfa1 -c jtag2isp   -P usb  -U hfuse:w:0x9c:m -U lfuse:w:0x62:m