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

Estimate the amount of work required here. Issues should represent approximately 1 to 3 days of work.

Sub-Issues

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• [ ] Add a checkbox for each sub-issue here.

Relevant Deadlines

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Funding Source

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Define the Metadata

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• [ ] Select Repository and/or Organization level Project(s) or add alert: NEED CYCLE ASSIGNMENT label
• [ ] Select Milestone as the next official version or Future Versions

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.
• [ ] Submit a pull request to merge into develop. Pull request: feature <Issue Number> <Description>
• [ ] Define the pull request metadata, as permissions allow. Select: Reviewer(s) and Development issues Select: Repository level development cycle Project for the next official release Select: Milestone as the next official version
• [ ] Iterate until the reviewer(s) accept and merge your changes.
• [ ] Delete your fork or branch.
• [ ] Close this issue.