In this PR:

• some tests to improve coverage of command_builder
• new test files for run_util, including dummy config files.
• tests for pre_run_setup in run_util.py. Tests for other function will follow in a futrue PR

Pull Request Testing

• Describe testing already performed for these changes:
  
  Tests passing locally

• Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:
  
  Nothing specific - more options/items could be added to the test config files if there's specific functionality to test

• Do these changes include sufficient documentation updates, ensuring that no errors or warnings exist in the build of the documentation?
  yes

• Do these changes include sufficient testing updates? [Yes or No]

• Will this PR result in changes to the test suite? [Yes or No]
  
  Yes - extra tests will run for run_util and command_builder

• Please complete this pull request review by [Fill in date].
  

Pull Request Checklist

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• Complete the PR definition above.
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  Select: @georgemccabe
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