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hapi-fhir-base-1.0 doesn't support having links in the BundleEntry which is not compliant to the spec #178
We are using hapi-fhir-base-1.0, and we checked the source code of ca.uhn.fhir.parser.ParserState.BundleEntryState
Seems like it doesn't support having link in the BundleEntry
Thanks for reporting! Committing a fix now.
Note that you might want to consider using the DSTU2 resource bundle (