Move from an options dict to a "config" (or similar) dict

[konklone]

Have all environment-wide configuration move into a variable (probably a dict, like it exists today), which has values from the CLI, values derived from those CLI flags, values from env vars, etc.

One config (or similarly named) thing that has this data. This could be instantiated at the top of the scan and gather files, and instantiated as part of the (planned) class-based approach to individual gatherers and scanners (who could access it as e.g. self.config).