I'm trying to create a single .ELF file that combines the bootloader with the blink sketch so I can burn both at the same time and set the fuses all in one operation in Atmel Studio, but in version 6.2 there is no option to save an .ELF production file. I know version 4 had this capability, but I don't think it has support for the SAMD21.
I managed to combine the bootloader and application into a single .HEX file by uploading the sketch after burning the bootloader and then downloading the .HEX from the chip, but obviously this doesn't include the fuse settings.