I looked into this and think I have a solution that should work for all SDL2 apps (like the latest EmulationStation) without having to recompile SDL. Instead of patching SDL, you can apply a udev rule to configure the retrogame.c input device to look like a keyboard to SDL2. More details are in the comment here: https://github.com/adafruit/Adafruit-Retrogame/issues/5#issuecomment-50083508
The basic idea is to create the file /etc/udev/rules.d/10-retrogame.rules and add this line to it:
does tonys fix still work? i bought most the parts for my project and wanted to use gpio for input with retropie 3. after i found this post i am woundering if this fix still works or do i need to do something else like get a teensy or the controlboard sold here.
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