ISPN-4458 Query DSL: negation predicates on properties of embedded entities are not correctly evaluated for non-indexed queries

Fixes following tests:
* ProtobufMatcherTest.testCollectionIsNotNull1
* AbstractMatcherTest.testProjectionOnRepeatedAttribute
* NonIndexedQueryDslConditionsTest.testProjectionOnOptionalField
* NonIndexedQueryDslConditionsTest.testSampleDomainQuery20

Link disabled tests to HQLPARSER-44
ISPN-4457 Update query tests to use the new index config api introduced with ISPN-3514
ISPN-4483 Replace usages of deprecated junit.framework.Assert with org.junit.Assert