Unit Test work - still cannot get Dstu3 working after several attempts, but included the skelton of a test to capture the effort anyways.

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.cql.provider.CqlProviderLoader;
+import ca.uhn.fhir.empi.provider.EmpiProviderLoader;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
@@ -97,6 +99,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired
   ApplicationContext myApplicationContext;
 
+  // These are set only if the features are enabled
+  private CqlProviderLoader cqlProviderLoader;
+  private EmpiProviderLoader empiProviderLoader;
+
   public BaseJpaRestfulServer() {
 
   }
@@ -121,10 +127,21 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
 
     setFhirContext(fhirSystemDao.getContext());
+
+    FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
+    if (fhirVersion == FhirVersionEnum.DSTU3 || fhirVersion == FhirVersionEnum.R4) {
+      if (appProperties.getCql_enabled()) {
+        cqlProviderLoader = myApplicationContext.getBean(CqlProviderLoader.class);
+        cqlProviderLoader.loadProvider();
+      }
+      if (appProperties.getEmpi_enabled()) {
+        empiProviderLoader = myApplicationContext.getBean(EmpiProviderLoader.class);
+        empiProviderLoader.loadProvider();
+      }
+    }
     registerProviders(resourceProviders.createProviders());
     registerProvider(jpaSystemProvider);
 
-    FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
     /*
      * The conformance provider exports the supported resources, search parameters, etc for
      * this server. The JPA version adds resourceProviders counts to the exported statement, so it