Refactor ApplicationConfiguration serialization for deprecated/modern settings and add tests for configuration behavior

[mrsuciu]

Refactor ApplicationConfiguration serialization for deprecated/modern settings and add tests for configuration behavior

Proposed changes

Added serialization guards and tests to ensure "legacy" configs stay marked deprecated and modern configurations stay "non-deprecated".

Related Issues

• Fixes Serializing and deserializing a "legacy" or "modern" configuration does not preserve SecurityConfiguration.IsDeprecatedConfiguration flag #3414

Types of changes

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• Bugfix (non-breaking change which fixes an issue)
• Enhancement (non-breaking change which adds functionality)
• Test enhancement (non-breaking change to increase test coverage)
• Breaking change (fix or feature that would cause existing functionality to not work as expected, requires version increase of Nuget packages)
• Documentation Update (if none of the other choices apply)

Checklist

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• I have read the CONTRIBUTING doc.
• I have signed the CLA.
• I ran tests locally with my changes, all passed.
• I fixed all failing tests in the CI pipelines.
• I fixed all introduced issues with CodeQL and LGTM.
• I have added tests that prove my fix is effective or that my feature works and increased code coverage.
• I have added necessary documentation (if appropriate).
• Any dependent changes have been merged and published in downstream modules.

Further comments

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 59.99%. Comparing base (d25caff) to head (f2836ca).
⚠️ Report is 58 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3415      +/-   ##
==========================================
+ Coverage   51.86%   59.99%   +8.12%     
==========================================
  Files         370      377       +7     
  Lines       78618    78754     +136     
  Branches    13650    13716      +66     
==========================================
+ Hits        40779    47250    +6471     
+ Misses      33705    27127    -6578     
- Partials     4134     4377     +243     

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