// MANIFEST.MF
Manifest manifest = addDigestsToManifest(inputJar);
je = new JarEntry(JarFile.MANIFEST_NAME);
je.setTime(timestamp);
outputJar.putNextEntry(je);
manifest.write(outputJar);

    /** Add the SHA1 of every file to the manifest, creating it if necessary. */
    private static Manifest addDigestsToManifest(JarFile jar)
            throws IOException, GeneralSecurityException {
        Manifest input = jar.getManifest();
        Manifest output = new Manifest();
        Attributes main = output.getMainAttributes();
        if (input != null) {
            main.putAll(input.getMainAttributes());
        } else {
            main.putValue("Manifest-Version", "1.0");
            main.putValue("Created-By", "1.0 (Android SignApk)");
        }

        BASE64Encoder base64 = new BASE64Encoder();
        MessageDigest md = MessageDigest.getInstance("SHA1");
        byte[] buffer = new byte[4096];
        int num;

        // We sort the input entries by name, and add them to the
        // output manifest in sorted order.  We expect that the output
        // map will be deterministic.
        TreeMap<String, JarEntry> byName = new TreeMap<String, JarEntry>();

        for (Enumeration<JarEntry> e = jar.entries(); e.hasMoreElements(); ) {
            JarEntry entry = e.nextElement();
            byName.put(entry.getName(), entry);
        }

        for (JarEntry entry: byName.values()) {
            String name = entry.getName();
            if (!entry.isDirectory() && !name.equals(JarFile.MANIFEST_NAME) &&
                !name.equals(CERT_SF_NAME) && !name.equals(CERT_RSA_NAME) &&
                (stripPattern == null ||
                 !stripPattern.matcher(name).matches())) {
                InputStream data = jar.getInputStream(entry);
                while ((num = data.read(buffer)) > 0) {
                    md.update(buffer, 0, num);
                }

                Attributes attr = null;
                if (input != null) attr = input.getAttributes(name);
                attr = attr != null ? new Attributes(attr) : new Attributes();
                attr.putValue("SHA1-Digest", base64.encode(md.digest()));
                output.getEntries().put(name, attr);
            }
        }

        return output;
    }