In Eclipse Galileo (3.5) or Ganymede (3.4) or older version, you can control the project packaging structure via the “Java EE Module Dependencies ” option, so that the project dependencies are deployed to the correct folder.
However, in the latest Eclipse Helios (3.6) , the “Java EE Module Dependencies ” is replaced by “Web Deployment Assembly “, which provide more powerful and flexible ways to configure the project packaging structure.