It seems like the Serial Port setting is used both for talking to the programmer, and for talking to the board when using bootloader and/or serial monitor.
Typically, these are actually different ports, right?
I can't find a way to force a particular serial port in the programmer.txt file, either.
What's a good solution for this?
theres only one serial port on the arduino, the programmer is the bootloader. when the avr first comes up it runs the bootloader, which waits a second or two for stk500 commands, if it receives some it kicks into programmer mode, if not it moves on to your program.
I understand there is only one serial port on the Arduino. I'm talking about when using a separate programmer -- which there is a lot of support for in the IDE.
However, that support falls surprisingly short in this one place.