Merge configuration files and clean up option paths

[kennytv]

This issue will be used to track the current progress and provide info on changes.

https://github.com/PaperMC/Paper/tree/feature/config-merge contains the current progress on merging and upgrading the config, with a small number of renames and removals.

More detail will be added later.

[Keeg-Turner]

Quick question from a curious server admin: will the merger include server.properties?