Refactor how Questionnaires are generated during the $apply operation

[barhodes]

• The $apply operation will now always generate a Questionnaire from any action.input elements that reference a Profile. A populated QuestionnaireResponse will be returned with the generated Questionnaire contained within it.
• Generated Questionnaire items from StructureDefinitions that reference a CPG Feature Expression will now have an SDC Questionnaire Item Population Context extension with the expression. The expression name will be set to the name of the StructureDefinition.
• Added support for the SDC Questionnaire Launch Context extension in the $populate operation.
• $populate now correctly expects the subject parameter to be a Reference rather than a String.
• $populate will use "definition-based-population" with Item Population Context when the items have definitions.
• $extract now uses the Questionnaire item for definition based extraction, the QuestionnaireResponse definition will only be used if the Questionnaire cannot be found by the server.
• $extract now handles answers of type decimal or integer with a Questionnaire Unit extension correctly.
• $extract now handles multiple resources being returned by the Item Extraction Context expression.
• Added EvaluateProcessor for the Library/$evaluate operation.
• Fixed operation processors not using the proxy repository when endpoints are passed in.
• Added DataRequirementsVisitor and Processor for the $data-requirements operation.
• $data-requirements operation added for the following resources: Library, PlanDefinition, Questionnaire, ValueSet

Closes #472
Closes #481
Closes #482

[github-actions]

Formatting check succeeded!

[codecov]

Codecov Report

Attention: Patch coverage is 85.44251% with 176 lines in your changes missing coverage. Please review.

Project coverage is 72.95%. Comparing base (b78a391) to head (cd75a4f).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
...s/cqf/fhir/cr/visitor/DataRequirementsVisitor.java	86.20%	7 Missing and 9 partials ⚠️
...cqf/fhir/cr/plandefinition/apply/ApplyRequest.java	72.00%	4 Missing and 10 partials ⚠️
...onnaireresponse/extract/ProcessDefinitionItem.java	87.62%	3 Missing and 9 partials ⚠️
.../opencds/cqf/fhir/cr/library/LibraryProcessor.java	60.00%	6 Missing and 4 partials ⚠️
...questionnaire/populate/ProcessItemWithContext.java	90.74%	5 Missing and 5 partials ⚠️
.../cr/inputparameters/r4/InputParameterResolver.java	84.74%	4 Missing and 5 partials ⚠️
.../cr/inputparameters/r5/InputParameterResolver.java	84.74%	4 Missing and 5 partials ⚠️
...nnaireresponse/QuestionnaireResponseProcessor.java	76.31%	4 Missing and 5 partials ⚠️
.../cqf/fhir/cr/library/evaluate/EvaluateRequest.java	75.75%	4 Missing and 4 partials ⚠️
...qf/fhir/cr/questionnaire/populate/ProcessItem.java	83.33%	4 Missing and 4 partials ⚠️
... and 22 more

Additional details and impacted files

@@             Coverage Diff              @@
##             master     #505      +/-   ##
============================================
+ Coverage     72.87%   72.95%   +0.07%     
  Complexity       19       19              
============================================
  Files           363      365       +2     
  Lines         18710    19308     +598     
  Branches       2880     2949      +69     
============================================
+ Hits          13635    14086     +451     
- Misses         3711     3800      +89     
- Partials       1364     1422      +58     

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[Capt-Mac]

decent handful of issues flagged, don't see anything majorly critical, but I'd have a look through https://sonarcloud.io/project/issues?id=cqframework_clinical-reasoning&pullRequest=505&issueStatuses=OPEN,CONFIRMED&sinceLeakPeriod=true before merging

[barhodes]

decent handful of issues flagged, don't see anything majorly critical, but I'd have a look through https://sonarcloud.io/project/issues?id=cqframework_clinical-reasoning&pullRequest=505&issueStatuses=OPEN,CONFIRMED&sinceLeakPeriod=true before merging

Fixed all of them but the too many parameters in methods. Those will have to wait for another refactor.

[sonarcloud]

Quality Gate passed

Issues
0 New issues
14 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud