Excuse me for beeing an idiot. But how do you compile the bootloader from source? Do you do it from Atmel studio or from Arduino IDE. And how is it done? When I compile it in Atmel studio it gets an base adress of 0x0000 which is wrong.
I am used to program in assembler in Atmel studio and when I program in C i don't touch anyting else than the .c file. So some form of tutorial kind of thing would be helpful.