The arguments passed into Apply, Refresh, Diff could be modified which
caused the shadow comparison later to cause errors. Also, the result
should be deep copied so that it isn't modified.
This is necessary so that the shadow version can actually keep track of
what provider is used for what. Before, providers for different alises
were just initialized but the factory had no idea. Arguably this is fine
but when trying to build a shadow graph this presents challenges.
With these changes, we now pass an opaque "uid" through that is used to
keep track of the providers and what real maps to what shadow.
