I know this question has probably been asked a dozen times, and I'm sorry, but I have never actually found a satisfactory answer, so I figured I'd ask it myself to get clarification.
Is there a way to debug a bootloader and application combo at the same time if they are built as separate projects? I'm currently using AVR Studio, but I could get a different tool if need be.
I have combined the two hex files as described elsewhere on the forum and flashed the chip with that, but I'd really like to get in there with my JTAG and make sure everything is working. Can it be done Freaks?