Since a planned destroy can no longer indicate it is a full destroy,
unused values were being left in the apply graph for evaluation. If
these values contains interpolations that can fail, (for example, a
zipmap with mismatched list sizes), it will cause the apply to abort.
The PrunUnusedValuesTransformer was only previously run during destroy,
more out of conservatism than for any other particular reason. Adapt it
to always remove unused values from the graph, with the exception being
the root module outputs, which must be retained when we don't have a
clear indication that a full destroy is being executed.