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Add specifics to API level documentation #100

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@frank1010111

I am nearly complete with my JOSS review (openjournals/joss-reviews#10124) with the last checkmark being "Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?"

The examples section is spectacular, with explanations of what you can do with various commands, example commands, note and tip call-outs, and results. I would love to see the same for the API documentation. For instance, here in main I would like to see the command line arguments listed with an explanation of what they do.

An explanation of the common keys and values in dic would be super-helpful for contributors and people wanting to customize functionality.

For check_cmdargs knowing what command flags are being checked could be handy.

In, say coarser_grid how do you modify dic to set how much to coarsen the grid?

How does add_lost_pv_to_bundary_cells work? When do you call it?

And similar questions for the functions exposed by the API.

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