(PUP-1811) Fix collection use of include?

The virtual resource collection uses the comparator for include?, but a 
previous commit changed the signature. This wasn't caught until the 
acceptance tests ran because it turns out that the collection tests were not
being run against the future parser.

This fixes the problem by passing the scope that is available for collection
to the method. It also removes two of the acceptance tests in favor of adding
a new integration test and running the collection tests with the future
parser.