Move manipulation of the X stack to MetaStackTracker

Since MetaStackTracker is the code that knows about the current X stacking order
and the relationship between X windows and Wayland windows, it's cleaner to
encapsulate stack manipulation in MetaStackTracker rather than have the calling
code make the X calls and only call into MetaStackTracker to inform it about
the changes.

https://bugzilla.gnome.org/show_bug.cgi?id=736559