Fix for #3382 -- Empty classes as graph placeholders

As Brice discovered, the problem was that we simply ignored empty classes in
the graph when determining application order. This patch instead replaces them
with a resource of a new type which we've frequently noted the (internal) need
for: a whit, the smallest possible resource, which has no properties or other
semantics apart from its existence and its name.

This resource then ensures application order through the normal mechanisms.