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Update configuration documentation #559

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ClarkMcGrew
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This tries to capture the most recent state of the YAML for the configuration files and is moving
toward providing a user guide with recommendations.

I'm making this into a pull request so that it's more visible within the repository, but it will "never" be
ready so people should pull the branch and add changes as they are able.

This tries to capture the most recent state of the YAML for the
FitterEngine class.
@ClarkMcGrew
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In case my comment about "never" ready is misunderstood. Documentation can always be improved, but at some
point in the future we should start merging this branch!

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