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
Object[] children;
		try {
			children= pkgFragment.getChildren();
			for (int i= 0; i < children.length; i++)
				exportElement(children[i], progressMonitor);
			children= pkgFragment.getNonJavaResources();
			for (int i= 0; i < children.length; i++)
				exportElement(children[i], progressMonitor);
		} catch (CoreException e) {
			
			addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.errorDuringExport", pkgFragment.toString()), e); 
		}
	}
	private void exportContainer(IProgressMonitor progressMonitor, IResource resource) throws java.lang.InterruptedException {
		IResource[] children= null;
		try {
			children= ((IContainer) resource).members();
		} catch (CoreException e) {
			
			addWarning(JarPackagerMessages.getFormattedString("JarFileExportOperation.errorDuringExport", resource.getFullPath()), e); 
		}
		for (int i= 0; i < children.length; i++)
			exportElement(children[i], progressMonitor);
	}
	private void exportResource(IProgressMonitor progressMonitor, IPackageFragmentRoot pkgRoot, boolean isInJavaProject, IResource resource, IPath destinationPath, boolean isInOutputFolder) {
		boolean isNonJavaResource= !isInJavaProject || pkgRoot == null;
		boolean isInClassFolder= false;
		try {
			isInClassFolder= pkgRoot != null && !pkgRoot.isArchive() && pkgRoot.getKind() == pkgRoot.K_BINARY;
		} catch (JavaModelException ex) {