IPA generator removes references to contained resources

[xmhorsehead]

Describe the bug
In the IPS generator, the references are cleared out when it's pointing to resources that are not included in the bundle. However, this clears out resources that are contained as well. This creates a problem when Medication[x].medicationReference points to a contained Medication resource (which I assume is a common approach?).

To Reproduce
Steps to reproduce the behavior:

1. Turn on IPA generation in HAPI JPA Server.
2. Add a Medication[x] resource eg. MedicationStatement with medicationReference point to a contained Medication resource to a Patient.
3. Call $summary operation on the patient.
4. In the response, the reference to the contained Medication resource has been removed. This also made them inaccessible in narrative generation.

Expected behavior
The reference to contained resource should not be removed, as they are included in the bundle.

Environment:

• Current master of HAPI JPA STARTER project and HAPI FHIR