I was able to fork a project on GitHub and get it setup in eclipse, but I have a problem with the source folders. Basically, it's putting all the packages at the root of the source folder rather than building the proper hierarchy. Here is a screenshot that shows the issue I am having: 
I want it to combine all of the packages in to a top level com package, and then under that is the sk89q package, and then under that there should be the bukkit, jnbt, util, worldedit, etc packages. How can I accomplish this?