Recently, Koush released CWM Superuser to the world. It’s a super user app that allows you to choose what apps get root access, but it has the advantage of being open source and easily built from source without dependencies. This made it the prime candidate for CyanogenMod’s default SU app, so they decided to use it in their new nightlies. However, they did take it one step further.
You won’t find the app icon in your drawer anymore, because it’s been integrated into Settings. It’s under System and will offer the same functionality as the app interface, but is just a cleaner implementation. So if you notice the icon disappear after a CM update, don’t fret.