If you're looking to swap the Ctrl + Cmd keys in Ubuntu 16.04 either just because, or because you're using VirtualBox with an Ubuntu guest and an OSX host, then the answer you're looking for is here. Courtesy of Joel Koh.
- Launch terminal
- Edit X Keyboard Extension
nano /usr/share/X11/xkb/symbols/pc
- Make the following changes. Ensure your file looks like this:
modifier_map Control { Control_L, Control_R, Super_L, Super_R };
- Clear xkb's cache or reboot
rm -rf /var/lib/xkb/*