Answer by kmsquire for Reliably remapping keys per input device

I also wanted to do swap cmd and alt keys only on my MacBook Pro, but not when I have a normal external keyboard plugged in.

From the directions here, the following "just works" on 14.04 (and likely 13.10):

1. Add options hid_apple swap_opt_cmd=1 to /etc/modprobe.d/hid_apple.conf, creating the file if it doesn't exist
2. Rebuild initramfs with sudo update-initramfs -u -k all
3. Reboot