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I also took a look at the code from avrdude directly and i think it would be possible but i'm afraid borking my arduino / crius in the process :) don't know if i can make it unflashable somehow.
for example the apm_planner (extended version of qground control) uses avrdude again. i will raise an issue there and ask if they plan to use it nativ. flashtool and apm_planner are both c++ and qt so it would be easy to share it between the projects.
FlashTool currently compiles on these Platforms, but avrdude.exe is hardcoded.
We need a switch to call the correct avrdude executable by platform.
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