See PHI568. If you make the file tree UI very wide so that the page generates a horizontal scrollbar and then scroll the page, the page content can paint underneath the menu.

The menu already has a z-index to make it render above the content, but doesn't actually have a background. Give it a background.

The "transparent" rule was added in D16346 but I don't see any reason why we actually need it there, so I think this probably won't break anything.