Config file documentation

[TeaganKing]

This PR brings in additional documentation to describe our configuration file in order to clarify this setup information for CUPiD for users. This addresses #107.

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We could also use the key metrics configuration file as an example if there is a preference for that.

[TeaganKing]

Yes, I think that's a good idea. The images are rendering correctly now, but I'll update them to use the key metrics config file.

[TeaganKing]

Here's updated screenshots using the key metrics configuration file.