This change is necessary to remove the package instance (I) from Var
(issue #4142).  One of the main uses of the package instance is when varPI is
called by the linking phase in order to get the dependencies introduced by flags
and stanzas.  The validation phase also needs to look up dependencies introduced
by flags and stanzas, but it does so by looking up the dependencies once when it
chooses a package and then storing the dependencies in a map.  I refactored the
linking phase to also store dependencies in a map.