feat: read and write YAML config files

[kentquirk]

Which problem is this PR solving?

• The command-line configuration is getting a little out of hand, so we're adding the ability to read config files.

Short description of the changes

• Add a Global section to config
• Add --writecfg flag to allow writing the actual configuration to a YAML file
• Add --config to allow reading config out of a YAML file
• Add all the decorations needed to process this properly, including identifying parameters that should not be loaded from (or written to) a config file.
• Make it so that additional fields also work to be specified in the config file
• Various changes to make it all work (like parsing the fields)
• Update docs

[kentquirk]

This is the first step to solving #54