Comment 3 for bug 1081674

In 12.04 we changed unity-2d quite a bit. Before the launcher & dash were separate applications, and each had their own window. There was no XShaping being used before 12.04, so this problem would not have happened before that release.

We wanted the ability to draw anything anywhere on screen, hence this work. It made the HUD much easier, and the keyboard shortcuts popup was thus easy to do too (just didn't land before feature freeze).

A handy reference on compositing in my bookmarks is this:
http://web.archive.org/web/20100105155103/http://ktown.kde.org/~fredrik/composite_howto.html
And the XShape API is here
http://linux.die.net/man/3/xshapecombinemask

You'll need to dig into X.org's sources to find the implementation. Good luck!