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

After this, 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