Update documentation for scripts

[jtniehof]

This PR updates documentation for all our scripts.

• Fixes the formatting so the scripts docs actually build
• Updates and/or adds documentation for all scripts so that they are up to date

Note that the documentation of configuration file formats for certain scripts is still incomplete--that can't really be fully documented until I have written up the dbprocessing concepts document (so the config docs can link to, say, the definition of a process.)

PR Checklist

• [X] Pull request has descriptive title
• [X] Pull request gives overview of changes
• [X] (N/A) New code has inline comments where necessary
• [X] (N/A) Any new modules, functions or classes have docstrings consistent with dbprocessing style
• [X] (N/A) Major new functionality has appropriate Sphinx documentation
• [X] (N/A) Added an entry to release notes if fixing a major bug or providing a major new feature
• [X] (N/A) New features and bug fixes should have unit tests
• [X] (N/A) Relevant issues are linked in the description (use Closes # if this PR closes the issue, or some other reference, such as See # if it is related in some other way)

[jtniehof]

The diff on this is horrible; this is one of those that may be easier to read either by just looking at the final file, or looking at each individual commit.