Add refinediag and preanalysis capability

[ceblanton]

Describe your changes

Refinediag and preanalysis scripts nearly worked properly in the distant past. In the recent YAML era, they have not.

Issue ticket number and link (if applicable)

#701

Checklist before requesting a review

• I ran my code
• I tried to make my code readable
• I tried to comment my code
• I wrote a new test, if applicable
• I wrote new instructions/documentation, if applicable
• I ran pytest and inspected it's output
• I ran pylint and attempted to implement some of it's feedback
• No print statements; all user-facing info uses logging module

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