WSAD stores files inside the project directory, one of which is called ".classpath" and is used to store the list of JARs, etc that represent the class path for building that project. To change this, in WSAD, right click on the project in any of the perspectives and choose Properties. Then take a look at the Build Paths section. You can edit class path entries here.
Apologies if this isn't exactly correct, I don't have access to WSAD today.