I have a reference to the world, and I want to duplicate that world? Would I use Java Files? Is there some sort of bukkit way I can use it?
I would duplicate the world files and then import the new world into the server itself. Otherwise you can create a new world directly but youll need to setup everything manually (setting the worldseed, world generator, world type, etc.)
I think you can do that with Multiverse-Core Another option is create a new folder with the world name and copy the files one by one
