In order to swap the Command and Control keys on Macs that are running a Linux operating system, place the following lines in a file named .Xmodmap in your home directory:

remove Mod4 = Super_L
remove Control = Control_L
keysym Control_L = Super_L
keysym Super_L = Control_L
add Mod4 = Super_L
add Control = Control_L

Simply logout and log back in to activate the changes. If you do not wish to log out, you can activate the changes by typing the following command in a terminal:

xmodmap ~/.Xmodmap