With the recent version of SNESDev, you need to run ./build from within the directory /home/pi/RetroPie/supplementary/SNESDev-Rpi/. After the compilation has finished, you need to copy the new executable to /usr/local/bin via

sudo cp "/home/pi/RetroPie/supplementary/SNESDev-Rpi/SNESDev" /usr/local/bin/

and restart SNESDev via

sudo service SNESDev restart

I know that this should be easier – in the best case the button behavior could also be configured via the config file. But I did not find the time to implement that feature yet.