I want to use Caps Lock for the Hyper key because I need it in Emacs, so in /etc/default/keyboard I use the relevant XKBOPTIONS.
However, Unity seems to react to both: even though it passes Hyper_L through so it works in Emacs, the launcher and/or the HUD keeps popping up. I thought this was happening because xmodmap shows that both of them are assigned to mod3, so I ran xmodmap with
clear Mod3
clear Mod4
add Mod3 = Hyper_L
add Mod4 = Super_L
which now works, but I am under the impression that xmodmap is deprecated. Is there a way I can achieve the same with XKBOPTIONS?
EDIT I forgot to mention that I am asking this because xmodmap settings are lost when I switch layouts.