fix: OutputFolder path issue when both `output` and `dest` properties are specified

[filzrev]

This PR intended to fix issue #8967

Currently when both output and dest properties are specified. It's resolved to {baseDir}/{output}/{dest} path.

It cause problems when specifying dest on config and using --output parameter.

This PR changes this behavior to use output if it's specified by config/parameter. And only use the dest property if the `output' parameter is not specified.

Additionally following changes are included in this PR.

• Add [Obsolete] attribute to dest property.
  • It seems a lot of user using dest property. So it shouldn be removed after Json schema validation logics are integrated.
• Modify existing tests that use dest property. And add warning suppressions that use dest property.
• Change new TemplateManager's constructor parameter to use baseDirectory (No behavior changes)
• Remove unused optionsBaseDirectory variable and comments.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 53.84615% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 78.91%. Comparing base (fe673ec) to head (0051a98). Report is 183 commits behind head on main.

Files	Patch %	Lines
src/Docfx.App/PdfBuilder.cs	0.00%	4 Missing :warning:
src/Docfx.App/RunBuild.cs	80.00%	0 Missing and 1 partial :warning:
src/Docfx.Dotnet/DotnetApiCatalog.cs	75.00%	0 Missing and 1 partial :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #9975 +/- ## ========================================== + Coverage 74.31% 78.91% +4.59% ========================================== Files 536 540 +4 Lines 23189 23434 +245 Branches 4056 4059 +3 ========================================== + Hits 17234 18494 +1260 + Misses 4853 3802 -1051 - Partials 1102 1138 +36 ```

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