Well, I think we're hitting the home stretch here.
I've folded in most of the main functional changes, including
scrolling, pop-up menus, in-place editing of layer names, and not
rebuilding the entire tree every time you select a different layer.
Depending on how robust things are, I may be able to add the eye and
lock icons, and to switch the status bar's layer selector to use the
same layer manager back-end. However, any poking at it people can do
in the mean time would be helpful.