Finish remaining tasks for #2460

[georgemccabe]

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
• Other tasks?

Time Estimate

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Issues should represent approximately 1 to 3 days of work.

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Define Related Issue(s)

Consider the impact to the other METplus components.

• METplus, MET, METdataio, METviewer, METexpress, METcalcpy, METplotpy

Task Checklist

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• Complete the issue definition above, including the Time Estimate and Funding Source.
• Fork this repository or create a branch of develop.
  Branch name: feature_<Issue Number>_<Description>
• Complete the development and test your changes.
• Add/update log messages for easier debugging.
• Add/update unit tests.
• Add/update documentation.
• Add any new Python packages to the METplus Components Python Requirements table.
• Push local changes to GitHub.
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• Close this issue.