Like in a very non-technical way if someone had a mining laser and they right-clicked normally it would say hey server player right-clicked and the server goes hmm he had a mining laser in his hand so Im supposed to fire the laser and remove some energy, so it does, but with plugins when someone does something like enters a worldguard region it first says hey bukkit does player have the permission node worldguard.randomstuff.bypass.region-a and bukkit says either yes or no and when you list the plugins using /plugins or /pl it includes all the mods and the mods were ported to use bukkit methods like the ones to add recipes and stuff so Im guessing it can also ask bukkit about permission so instead of going Im supposed to fire the laser it first says hey bukkit does player have ic2.laser.use and if it does it proceeds otherwise it stops and tells them you dont have permission to fire a laser, theres probably also a way to add this for recipes so it checks ic2.laser.craft for example. Of course decompiling it and sorting through and modifying a bunch of code would be required for all this because ic2 and ee are derpy and unlike other less derpy mods doesnt break blocks as a player (that reminds me you need to give computercraft permission to break blocks because turtles dont work, just add a user called ComputerCraft and give them the member group or something).