Preparatory refactors and deprecations for ValidationContext split

[dotasek]

This refactors some of the code used to generate ValidationEngine instances for tasks in the CLI and in the validator-wrapper project.

Its primary purpose is to move ValidationContext processing code into fewer places to enable replacement with more modular POJOs. Before ValidationContext is completely removed, methods can be put in these places to derive those modular POJOs to ensure backward compatibility.

[dotasek]

Including this question from @grahamegrieve so we can track design decisions.

do we use any of the deprecated methods?

Yes. ValidationContext is used to pass params from the CLI and from validator-wrapper. These should be maintained to give downstream projects like matchbox and Inferno (@oliveregger, Inferno Contact?) a period to adjust.

The intent here is to eventually get rid of them and replace them in the following manner:

//Old way
ValidatorEngine engine = validationService.initializeValidator(validationContext, definitions, timetracker);

// Note that there's no option to change things like hintAboutNonMustSupport, anyExtensionsAllowed, etc. as these are pulled from the engine.
InstanceValidator instanceValidator = getValidator(FhirFormat.JSON);

//New way. Note that definitions is gone because of the changes in the PR, which automatically build it from validationEngineSettings.

ValidatorEngine engine = validationServive.buildEngine(validationEngineSettings, TimeTracker tt)

// Now we have a validationEngineSettings, which can be used to set hintAboutNonMustSupport, anyExtensionsAllowed, etc. So now an existing ValidationEngine has fewer reasons to change and is easier to re-use by things like server mode.
InstanceValidator instanceValidator = getValidator(validationInstanceSettings, FhirFormat.JSON);

What I was envisioning for backwards compatibility is that validationEngineSettings would contain a default validationInstanceSettings so that getValidator(FhirFormat.JSON) could just use that.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 13.34%. Comparing base (630bc69) to head (73c87c5).
⚠️ Report is 7 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff              @@
##             master    #2162      +/-   ##
============================================
- Coverage     13.35%   13.34%   -0.01%     
+ Complexity    37077    37061      -16     
============================================
  Files          2459     2459              
  Lines        724940   724941       +1     
  Branches     211969   211966       -3     
============================================
- Hits          96833    96764      -69     
- Misses       594960   595049      +89     
+ Partials      33147    33128      -19     

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