Well to start off you will need a permissions plugin like PermissionsEx or SimplePermissions. Then, simply give players permission to perform the actions you would like them to be able to do. So for example if you want players to be able to break stone blocks on your server you would give them the permission protectionPerms.block.break.minecraft:stone. If players don’t have the appropriate permission for an action they won’t be able to perform it!
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