Everyone who joins your server will be assigned permissions based on the default.json file located in the main directory (Permissions).
You can, of course, rename this file to something like "guest.json," but then you'll need to specify this new name in the server.properties file (at the very bottom) so that it's used as the default permissions file.
Group permissions belong in the "groups" folder... for example, admin.json and player.json
These group permissions can be assigned to players in-game by an administrator using the "setplayergroup" command.
i found an issue with using the default.json being in the base permissions directory. for some reason the default permission does not work when a player logs on and allows them to do admin stuff with plugins, like it passes the isAdmin() method. for a fix we renamed the default and placed it in the groups directory. we then made a new default in the permissions directory and set everything to false. glad you said something as i had forgot to mention this to red51
