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
}
		return count;
	}
	/**
	 * Exports the passed resource to the JAR file
	 *
	 * @param element the resource or JavaElement to export
	 */
	protected void exportElement(Object element, IProgressMonitor progressMonitor) throws InterruptedException {
		int leadSegmentsToRemove= 1;
		IPackageFragmentRoot pkgRoot= null;
		boolean isInJavaProject= false;
		IResource resource= null;
		IJavaProject jProject= null;
		if (element instanceof IJavaElement) {
			isInJavaProject= true;
			IJavaElement je= (IJavaElement)element;
			try {
				resource= je.getUnderlyingResource();
			} catch (JavaModelException ex) {
				addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.underlyingResourceNotFound", je.getElementName()), ex); 
				return;
			}
			jProject= je.getJavaProject();
			pkgRoot= JavaModelUtil.getPackageFragmentRoot(je);
		}
		else
			resource= (IResource)element;
		if (!resource.isAccessible()) {
			addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.resourceNotFound", resource.getFullPath()), null);