public static void main(String[] args) throws Exception {
    PDDocument pdf = null;
    try {
        System.out.println("argument:" + args[0]);
        pdf = PDDocument.load(new File(args[0]));
        addOverlay(pdf); //flattens overlay, fields lost.
        pdf.save("output.pdf");
        pdf.close();
    } finally {
        if (pdf != null) {
            pdf.close();
        }
    }
    return;
}

private static void mergeOverlay(final PDDocument pdf) throws IOException {
    PDDocument overlayPDF = PDDocument.load(new File("overlay.pdf"));
    Overlay overlay = new Overlay();
    overlay.overlay(overlayPDF, pdf);
}