Your right, aside from making sure that I/O pin is low on start up I can't really use the boot loader.
From what I can tell all the pins start LOW on boot, so I probably don't need to even modify the boot loader.
But assuming I do add that into the descriptors.c and the .h file for my board, what do you use to compile the .hex file.
Secondary question:
The goal is that when I press a button connected to a interrupt pin, it toggles the output on a different pin. But this is a background subroutine, not part of the sketch.
I need to figure out how to write my interrupt subroutine code to a memory slot ex. 0x002A that won't be overwritten by new sketches or conflicts with the bootloader.
If you use interrupts you do this all the time at the end of your main loop, I'm just trying to figure out how to have it stored outside the sketch memory.
Any ideas?