So to compile and upload you have this mouthful: arduino-cli compile --fqbn arduino:samd:mkr1000 Arduino/HackadayPgm arduino-cli upload -p /dev/ttyACM0 -fqbn arduino:samd:mkr1000 Arduino ...

I have been delving (groping blindfold, more accurately) into the Arduino compiler adaptation code to try to determine how it handles the switch-over between its pwm activities, its set-I/O-to-output ...