Remapped Control and Super are not respected by Unity

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http://askubuntu.com – I try to switch my left Control with left Super. I use xmodmap and it works, except that Unity seems to not respect the change. I guess it somehow bypasses the layer which xmodmap is modifying. Furthermore, I cannot really change the unity binding using CCSM, as it does not allow me to set old Control (now Super, which CCSM somehow recognizes as Primary). Any clues? (HowTos)