Bug 13799 JAR exporter exports class files from output folder
There was a problem with the output folder not being detected as such.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/jarpackager/JarFileExportOperation.java
try {
					resource= je.getUnderlyingResource();
				} catch (JavaModelException ex) {
					addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.underlyingResourceNotFound", je.getElementName()), ex); 
					return count;
				}
			}
			else
				resource= (IResource)element;
			if (resource.getType() == IResource.FILE)
				count++;
			else
				count += getTotalChildCount((IContainer)resource);
		}
		return count;
	}
	
	private int getTotalChildCount(IContainer container) {
		IResource[] members;
		try {
			members= container.members();
		} catch (CoreException ex) {
			return 0;
		}
		int count= 0;
		for (int i= 0; i < members.length; i++) {
			if (members[i].getType() == IResource.FILE)
				count++;
			else
				count += getTotalChildCount((IContainer)members[i]);