Refactor CLI & Standardize Configuration Naming Conventions

This branch does a couple things:

  • standardizes all command-line flags to use dashes
  • standardizes all configuration file keys use camel case
  • moves the configuration docs to CONFIGURATION.md and fills it out a bit
  • fixes a broken setting (--config_dir)
  • registers all commands with the DI container

It will be a breaking change for people using the settings that changed, but I think it'll be beneficial in the long run to make it all consistent.

I've had this branch sitting around for a while. I figured I would clean it up a bit and open a merge request. Feel free to request changes or reject.

Edited by Chris Brower

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