More syncing and QOL

[Byte-Nova]

This PR adds more NPC settlement syncing and some QOL changes into the mix of the mod.

• NPC settlements are now able to be completely destroyed and sync correctly with the rest of the planet, including new users.
• All configurable server files now have default values out of the box, so things like sites and events can work even if no settings have been saved.
• Overall code cleaning to make it easier to read and understand. Some classes have been separated into smaller ones for consistency.