For various reasons, I decided to try writing a SD card bootloader for my Ultimaker2.
The project is open source and on my GitHub here.
My goal was to install this new bootloader without having physical access to the circuitry. Thus I cannot use a ISP tool and must be done through the bootloader that is already present on the Ultimaker2. The only way to do this is to partition off a portion of application memory region for a secondary bootloader that executes after the original bootloader. But the ATmega2560 has a restriction that prevents anything in the application memory region from modifying the flash memory at all. Overcoming this restriction is what this hack is all about, continue reading if you are interested in learning more.