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Bukkit is a server managing program, not actually a server itself... You can have a server using Bukkit that's dedicated, On the other hand... you can have a server using Bukkit that isn't.
Minecraft commands were first seen in bukkit server. We do not know when the first commands were made for bukkit servers however
you cannot set up permissions in a normal minecraft server. you must have a bukkit server to use permissions. check the bukkit forum for more info.
You'll need a plugin to do so.