Enhancement: Refactor wrappers to consistently find input files

[georgemccabe]

EDIT: This issue originally covered both adding documentation for new config variables and updating all wrappers to consistently find input files using RuntimeFreq's functions. The new development work is out of the scope for the 6.0.0 release, so I created issue #2757 to update the documentation for the 6.0 release. Then I renamed this issue and moved it to 6.1 development.

The functionality for #2460 has been added and works as expected. However, there are some additional changes that should be done before the official release.

Describe the Task

• Update logic to find files to be consistent and use RuntimeFreq's functions

• Ensure unit tests still pass after above changes

• Add documentation for new config variables for allow missing input logic -- moved to issue Documentation: Add allow missing input variables to glossary #2757

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