Add stubs to dependency list

Kinda big regression, but stubbed assets weren't being added to the "stubber's" dependency list. So changes in the stub bundle wouldn't cause the source to be invalidated.

Initial commit has to special case the dependency paths metadata field which I don't like. I think I need to expose a more generic bundle reducer that will have access to the asset list before stubbed assets are removed

Fixes #652.

/cc @dgraham