Update Clinical Reasoning plugin (#692)

* Reproducing issues with CR/HAPI cds-hooks processing

* Add new $questionnaire operation

* Update StarterIpsConfig.java

* Update pom.xml

* Fixes for configuration properties

* Update VS Code launch properties

* Fixes for CQL logging

* Update pom.xml

* Remove unused threaded option

* Update to 7.1.7

* Fix some CR defaults

* Update to new snapshot

* Update pom.xml

* Fix test settings

* Do not make prefetch calls if all items are present

* Add alternative application.yaml for CDS settings.

* Add CdsHook tests and documentation

* Comment out custom prefetch until it is more mature

* Removal of DataEndpoint parameter is not longer needed

* Fix debug logging setting being overwritten

* Revert change

* Remove unused class

* Adding Rec10 Test

* Disable test until fixed

* fix tests

---------

Co-authored-by: c-schuler <hoofschu@gmail.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

.vscode/launch.json

@@ -7,7 +7,18 @@
             "cwd": "${workspaceFolder}",
             "mainClass": "ca.uhn.fhir.jpa.starter.Application",
             "projectName": "hapi-fhir-jpaserver-starter",
-            "args": "",
+            "vmArgs": [
+				"-XX:TieredStopAtLevel=1",
+				// "-Ddebug=true",
+				// "-Dloader.debug=true",
+				"-Dhapi.fhir.bulk_export_enabled=false",
+				"-Dspring.batch.job.enabled=false",
+				"-Dspring.main.allow-bean-definition-overriding=true",
+                "-Dhapi.fhir.cdshooks.enabled=true",
+				"-Dhapi.fhir.cr.enabled=true",
+				"-Dspring.main.allow-bean-definition-overriding=true"
+
+			],
             "envFile": "${workspaceFolder}/.env"
         }
     ]

.vscode/settings.json

@@ -5,5 +5,6 @@
         "**/.settings": true,
         "**/.factorypath": true
     },
-    "java.compile.nullAnalysis.mode": "disabled"
+    "java.compile.nullAnalysis.mode": "disabled",
+    "java.configuration.updateBuildConfiguration": "automatic"
 }