Command line options don't override config file

[dtwilliamson]

I'm not sure if the first run options set the values in files/config.json but subsequent runs seem to neither temporarily override them nor persistently overwrite them in the file.

[aunefyren]

If I remember correctly it does not override, only replace null values. This system should be overhauled now that I am doing a bunch of refactoring.

[dtwilliamson]

Perhaps there should be a hierarchy like command-line-options override environment-variables override config-file. I think a lot of software works that way.