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by X-Istence 5071 days ago
Except that XQuartz in the past installed itself to various system paths on Mac OS X. When you "upgrade" the OS the installer moves everything installed out of the way and basically does a clean install of the OS. At the end it copies over everything in paths that it doesn't control (mainly /Users, /usr/local, (/usr/<everything else> gets wiped), /Applications, /opt and others). Anything that is core to the OS will basically be in a clean install state.

For example, I've written some custom device drives for OS X that were installed in the system path (being kexts and all), those were removed. They weren't specifically compatible with OS X Mountain Lion, so it makes sense.