Windowing system on El Capitan, and XQuartz I've just installed XQuartz on my Macbook Pro Retina 13" which runs El Capitan, because a development tool I'm using required me to do so. I know that XQuartz is (kind of) like the new X11, supported by Apple through an open source community, but I'm confused as to what the relationship is between XQuartz and El Capitan.

Here is what I'm thikning. If I had to install XQuartz by hand, then clearly El Capitan was using some other windowing system. But what? Having now installed XQuartz, what's changed? Have I downgraded my El Capitan in any way? I haven't noticed anything different yet. Is it reversible?

By the way, I haven't yet set up time machine, and I now regret it.
XQuartz is a windowing system on its own, just installing it doesn't change anything. If you need to run application requiring X11/XQuartz, you need to start the Xquartz app (aka X11 server) before you start the application. The X11 server will then run "on top" of OS X, so the behaviour of other applications doesn't change.

See also What is XQuartz? for more details.