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How about remapping the keys? xmodmap should do the trick there.

Assuming that your command button is replaced with meta (I can't help you there, I don't own a Mac) this should work for you:

xmodmap -e "remove control = Control_L" xmodmap -e "remove mod4 = Super_L" xmodmap -e "add control = Super_L" xmodmap -e "add mod4 = Control_L"

This will work until you end your session.

Permanent solution

1. Make ~/.Xmodmap file.

2. Write this into it:

remove control = Control_L remove mod4 = Super_L add control = Super_L add mod4 = Control_L

3. You should now somehow put xmodmap ~/.Xmodmap to run at startup (I'm having trouble to find out how right now, will fix later).

You can learn more abour xmodmap xmodmap ArchWiki.