Ap/readme outputs

[austinhpatton]

Included a bunch of little changes to: 1) make the use of snake case more consistent across all publish directories and output filenames 2) clean up the publishdirs to remove extraneous, unwanted files or directories that are produced for internal purposes only or are persistent legacies of past versions 3) include a detailed description of the output directories and their contents. I imagine this is mostly just a draft, and can be tidied up, including referencing links to the github repositories of each software (where appropriate) for more detailed description of outputs, etc.

More still needs to be done with the readme (i.e. what is listed in the code cleanup PR, etc), but this is a start, and at least includes some cleanup of the outputs themselves.

[github-actions[bot]]

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