This is my procedure every time I start my computer:
xkeycaps -kbd mac
I then swap the downarrow and left shift keys, which in fact switches the Left-Command and Left-Option on my Mac keyboard.
Try as I may, I can't figure out how to automate this. I've tried using its xmodmap export feature, I've tried writing xmodmap files myself, but nothing has any effect.
I'm looking for a way to make this key exchange from the CLI so I can put it in a script.