Make VariableCollection handle both input and output variables.

VariableCollection now holds both the input and output variables.  To construct
a VariableCollection, two PartialVariableCollections are used that hold the
input and output variables.  The two are appropriately combined, while still
allowing the inputs and outputs to be separately pulled.

A single PartialVariableCollection also works, to allow for an input only
collection, which is useful for testing.