[This thread split off from: https://www.avrfreaks.net/index.p... ]
I do not see the purpose of overwriting the flash with the same content all over again
There's an option somewhere that only reloads the Flash when the object file has changed.
n FPGA chip with 500k gates and a soft core of an AVR, nobody is going to play with OCD, as you can add literally any functionality, timers, counters, and trigger on just any event you can even imagine.. But this is still off topic.
I've actually been there, and you really need a debugger too with a softcore on an FPGA ;) Nice touch is that you can also load the FPGA (along with your own logic) with a logic analyser with inputs and triggers of your choice. The JTAG is used as the comms channel.
One problem with an FPGA is that you really want to limit the number of debug/burn cycles of the logic (not the software which can be uploaded apart from the logic configuration). A recomplication of the logic can easily take hours.