Unify configuration, comment the options in config #197
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This PR removes the second configuration file so the users only have one place to look and we only have one place to update.
I have also started to add comments to the configuration file describing the configuration options available, and hopefully that can be the start of using it as the main documentation so we only have to update one thing.
I would appreciate if people would help me a bit by using GitHub Comments "suggestions" to add documentation strings to the options that are missing them (or improve my suggestions).