Does the compiler care about bootloader size?

If we change the bootloader size on an UNO, does the ino or hex file care about that? is there anything I have to change to compensate for the bootloader size change? I am using AVRdude and an ISP, so I do not care about programming over the "standard arduino method" over the USB port.

The flash size in boards.txt is just there to act as a sanity check to keep you from trying to upload something too big.

Also, the bootloader is only needed for uploading over serial (ex though onboard usb serial bridge on uno), and in fact, when you program with ISP, the bootloader typically gets removed. So if you're programming via ISP, there shouldn't be any bootloader involved at all.

So, if I compile something in the arduino environment, it should not care about the fact that I have a custom bootloader that now takes up 2kb (the new bootloader is used to upload over a different protocol bus)? I know my program is small enough (only takes up about 13kb), but it does not work when I upload it with my newer bootloader program. Obvioulsy, it could be my bootloader itself, but it would be much easier if teh issue was a parameter change.

Thanks

Aaaah, I see.

If you're uploading your program via ISP, you may be clobbering the bootloader when you upload it.

Also check fuses, particularly bootrst and the bootsz.

Do you know if your new bootloader is running? Does it think it's uploaded successfully? If so, dump the flash over ISP and see what it did wrong.

One more questions....

If we use AVRDude, is there a way to tell it to upload code over the ISP but not write over the bootloader space?

To do that, I think you need to change the address in the hex file to start somewhere beside the boot area.
Or create a combined file that loads the bootloader and the sketch.

Ok, so just doing a standard AVRDude command will wipe the bootloader out? If I take an Arduino, and program it via ISP, I probably no longer have the bootloader, correct?

Correct. File:Upload Using Programmer wipes out the bootloader.

File:Upload Using Programmer wipes out the bootloader

Flash memory has to be erased before it can be programmed with new data. The bootloader has access to an internal "erase page", so that it can erase a page at a time, but ISP programming doesn't have that (I don't know why not.) It can only erase the entire chip (which includes the bootloader section.)