Bukkit/Spigot configs and Paper's additions to them aren't documented

[Phoenix616]

Currently only the paper default and world configuration files are documented. The server generated other configs like bukkit.yml, spigot.yml and commands.yml too though so they should probably be documented as well. (Or at least linked in an obvious place)

Paper also adds values to those files (e.g. the wake-up-inactive for the entity activation range in spigot.yml is from Paper improvements to that feature) so at least those should be mentioned in the Paper docs.

[Nacioszeczek]

Partially fixed by #209, #221 and #230.
We should probably still explain commands.yml, help.yml and permissions.yml?
cc @olijeffers0n