This answer is mostly based on the answer given here. The reason I ask and answer this question again is the final step, which was not fully described. For further reading about xkb look here, here, and here.

1. Create a file in /usr/share/X11/xkb/symbols (could also be in /etc/X11/xkb/symbols) called altwin2 and containing the following mapping:

   
   
   

   // Control is SWAPPED with Win-keys 
   
   partial modifier_keys
   
   xkb_symbols "cmd_n_ctrl" {
   
       key <LWIN> {        [       Control_L               ]       };
   
       key <RWIN> {        [       Control_R               ]       };
   
       key <LCTL> {       [       Super_L         ]       };
   
       modifier_map Control { <LWIN>, <RWIN> };
   
       modifier_map Mod4 { <LCTL> };
   
   };
   
   




2. Insert the following line under the option = symbols section in /usr/share/X11/xkb/rules/evdev (disregard the warning on the first line):

   
   
   

   altwin2:cmd_n_ctrl               =       +altwin2(cmd_n_ctrl)
   
   




3. Add the new option to /usr/share/X11/xkb/rules/evdev.lst under the section option:

   
   
   

   altwin2:cmd_n_ctrl    Win swapped with Ctrl
   
   




4. If you don't know where your keyboard configuration file is, you can edit it using dconf-editor, adding "altwin2:cmd_n_ctrl" in xkb-options under org::gnome::desktop::input-sources as shown here. If you know where your configuration file is, you should include the new option in the XkbOptions field as shown below:

   
   
   

   Section "InputClass"
   
           Identifier "keyboard-layout"
   
           Driver "evdev"
   
           MatchIsKeyboard "yes"
   
           Option "XkbLayout" "us, ru, ca, fr"
   
           Option "XkbOptions" "altwin2:cmd_n_ctrl"
   
   EndSection
   
   




5. Either reboot or restart lightdm to update the changes:

   
   
   

   sudo restart lightdm
   
   

NOTE: if any changes are made directly in the layout files, i.e. not using options, the cached files in /var/lib/xkb/ need to be deleted as indicated here.