Added better command line documentation.

[Paul-Ferrell]

Pull Request Template

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Checklist

• My code follows the style guidelines of this project
• I have added/updated comments where needed
• I have added tests that prove my fix is effective or my feature works
• I have run make test (or equivalent) locally and all tests pass
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Description

Please include a summary of the change and which issue is fixed.
Also include relevant motivation and context.

Fixes #(issue)

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update

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