@User5115 what if I provide a HEX file and you upload it on command line ? You can do that on windows, linux and MAC. (if you rename the .arduboy file to .zip, you can extract the HEX file)
If you put on extra info while uploading (preferences) on the ARDUINO IDE, you can see what command you need to use for uploading with AVRdude.
and look for something like this:
/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude -C /Applications/Arduino.app/Contents/Java/hardware/tools/avr/etc/avrdude.conf -v -p atmega32u4 -c avr109 -P /dev/cu.usbmodem630 -b 57600 -D -U flash:w:/var/folders/ARDU_AB.ino.hex
you'll have to look for the correct "usbmodem" yourself