Before the sketch initiates an auto-reset for upload it pokes a magic word into a specific RAM address. On starting the bootloader checks this address. If it finds the magic word it knows the bootloader code should run. If not it jumps straight back to sketch.
Test in a sketch by adding to setup():
wdt_enable(WDTO_2S);
Sketch should upload, start, run for two seconds, WDT, and sketch should restart (not bootloader).
Had to cut out unused descriptor code to make the bootloader still fit in 4k.
Disconnect programmer after burning bootloader to get the full effect. ICSP and JTAG programmers do a hardware reset after any reset condition, confusing the firmware a little.
