I have a Yun Shield connected to a Mega2560. To upload a sketch I select 'Export compiled binary', which then places two .hex files in the sketch directory…one without the boot loader "…ino.mega.hex" and one with the boot loader "…ino.with_bootloader.mega.hex". The .hex file can then be loaded to the Mega2560 by logging into the Yun Panel and then select the board and .hex file for loading.
My question is: which file should be loaded to the Mega2560 with this method? The .hex without the boot loader or the .hex with the boot loader?