Document the interactions of permissions over command bases

[JorelAli]

new CommandAPICommand("hello")
  .executes(...)
  .register()

new CommandAPICommand("hello")
  .withPermission(...)
  .executes(...)
  .register()

Because these commands have the same name, the permission from the second one doesn't carry over. The fix is to apply the permission to the first argument. This should be documented!