java –jar signapk.jar [-w] publickey.x509[.pem] privatekey.pk8 input.jar output.jar

 public static void main(String[] args) {
 //...
 boolean signWholeFile = false;
 int argstart = 0;
 /*如果对ROM签名需传递-w参数*/
 if (args[0].equals("-w")) { 
  signWholeFile = true;
  argstart = 1;
 } 
 // ...
 try {
  File publicKeyFile = new File(args[argstart+0]);
  X509Certificate publicKey = readPublicKey(publicKeyFile);
  PrivateKey privateKey = readPrivateKey(new File(args[argstart+1]));
  inputJar = new JarFile(new File(args[argstart+2]), false); 
  outputFile = new FileOutputStream(args[argstart+3]);
  /*对ROM签名，读者可自行分析，和Apk饿签名类似，但是它会添加otacert文件*/
  if (signWholeFile) {
   SignApk.signWholeFile(inputJar, publicKeyFile, publicKey, 
    privateKey, outputFile);
  }
  else {
   JarOutputStream outputJar = new JarOutputStream(outputFile);
   outputJar.setLevel(9);
   /*addDigestsToManifest会生成Manifest对象,然后调用signFile进行签名*/
   signFile(addDigestsToManifest(inputJar), inputJar, 
   publicKeyFile, publicKey, privateKey, outputJar);
   outputJar.close();
  }
 } catch (Exception e) {
  e.printStackTrace();
  System.exit(1);
 } finally {
  //...
 }
}

Manifest-Version: 1.0
Created-By: 1.6.0-rc (Sun Microsystems Inc.)
 
Name: res/drawable-hdpi/user_logout.png
SHA1-Digest: zkQSZbt3Tqc9myEVuxc1dzMDPCs=
 
Name: res/drawable-hdpi/contacts_cancel_btn_pressed.png
SHA1-Digest: mSVZvKpvKpmgUJ9oXDJaTWzhdic=
 
Name: res/drawable/main_head_backgroud.png
SHA1-Digest: fe1yzADfDGZvr0cyIdNpGf/ySio=

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)");
 } 
 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) &&
   !name.equals(OTACERT_NAME) &&
   (stripPattern == null ||
    !stripPattern.matcher(name).matches())) {
   InputStream data = jar.getInputStream(entry);
   /*计算sha1*/
   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();
   /*base64编码sha1值得到SHA1-Digest属性的值*/
   attr.putValue("SHA1-Digest",
       new String(Base64.encode(md.digest()), "ASCII"));
   output.getEntries().put(name, attr);
  }
 } 
 return output;
}

public static void signFile(Manifest manifest, JarFile inputJar, 
File publicKeyFile, X509Certificate publicKey, PrivateKey privateKey,
 JarOutputStream outputJar) throws Exception {
 // Assume the certificate is valid for at least an hour.
 long timestamp = publicKey.getNotBefore().getTime() + 3600L * 1000;
 JarEntry je;
 // 拷贝文件
 copyFiles(manifest, inputJar, outputJar, timestamp);
 // 生成MANIFEST.MF
 je = new JarEntry(JarFile.MANIFEST_NAME);
 je.setTime(timestamp);
 outputJar.putNextEntry(je);
 manifest.write(outputJar);
 // 调用writeSignatureFile 生成CERT.SF
 je = new JarEntry(CERT_SF_NAME);
 je.setTime(timestamp);
 outputJar.putNextEntry(je);
 ByteArrayOutputStream baos = new ByteArrayOutputStream();
 writeSignatureFile(manifest, baos);
 byte[] signedData = baos.toByteArray();
 outputJar.write(signedData); 
 // 非常关键的一步 生成 CERT.RSA
 je = new JarEntry(CERT_RSA_NAME);
 je.setTime(timestamp);
 outputJar.putNextEntry(je);
 writeSignatureBlock(new CMSProcessableByteArray(signedData),
      publicKey, privateKey, outputJar);
}

private static void writeSignatureFile(Manifest manifest, OutputStream out)
  throws IOException, GeneralSecurityException {
 Manifest sf = new Manifest();
 Attributes main = sf.getMainAttributes();
 //添加属性
 main.putValue("Signature-Version", "1.0");
 main.putValue("Created-By", "1.0 (Android SignApk)"); 
 MessageDigest md = MessageDigest.getInstance("SHA1");
 PrintStream print = new PrintStream(
   new DigestOutputStream(new ByteArrayOutputStream(), md),
   true, "UTF-8"); 
 // 添加Manifest.mf的sha1摘要
 manifest.write(print);
 print.flush();
 main.putValue("SHA1-Digest-Manifest",
     new String(Base64.encode(md.digest()), "ASCII")); 
 //对MANIFEST.MF的各个段计算sha1摘要
 Map<String, Attributes> entries = manifest.getEntries();
 for (Map.Entry<String, Attributes> entry : entries.entrySet()) {
  // Digest of the manifest stanza for this entry.
  print.print("Name: " + entry.getKey() + "\r\n");
  for (Map.Entry<Object, Object> att : entry.getValue().entrySet()) {
   print.print(att.getKey() + ": " + att.getValue() + "\r\n");
  }
  print.print("\r\n");
  print.flush();
 
  Attributes sfAttr = new Attributes();
  sfAttr.putValue("SHA1-Digest",
      new String(Base64.encode(md.digest()), "ASCII"));
  sf.getEntries().put(entry.getKey(), sfAttr);
 } 
 CountOutputStream cout = new CountOutputStream(out);
 sf.write(cout); 
 // A bug in the java.util.jar implementation of Android platforms
 // up to version 1.6 will cause a spurious IOException to be thrown
 // if the length of the signature file is a multiple of 1024 bytes.
 // As a workaround, add an extra CRLF in this case.
 if ((cout.size() % 1024) == 0) {
  cout.write('\r');
  cout.write('\n');
 }
}

private static void writeSignatureBlock(
 CMSTypedData data, X509Certificate publicKey, PrivateKey privateKey,
 OutputStream out)
 throws IOException,
   CertificateEncodingException,
   OperatorCreationException,
   CMSException {
 ArrayList<X509Certificate> certList = new ArrayList<X509Certificate>(1);
 certList.add(publicKey);
 JcaCertStore certs = new JcaCertStore(certList); 
 CMSSignedDataGenerator gen = new CMSSignedDataGenerator();
 //签名算法是SHA1withRSA
 ContentSigner sha1Signer = new JcaContentSignerBuilder("SHA1withRSA")
  .setProvider(sBouncyCastleProvider)
  .build(privateKey);
 gen.addSignerInfoGenerator(
  new JcaSignerInfoGeneratorBuilder(
   new JcaDigestCalculatorProviderBuilder()
   .setProvider(sBouncyCastleProvider)
   .build())
  .setDirectSignature(true)
  .build(sha1Signer, publicKey));
 gen.addCertificates(certs);
 CMSSignedData sigData = gen.generate(data, false);
 
 ASN1InputStream asn1 = new ASN1InputStream(sigData.getEncoded());
 DEROutputStream dos = new DEROutputStream(out);
 dos.writeObject(asn1.readObject());
}

Keytool -genkey -alias fantongyo.keystore -keyalg RSA -validity 20000 -keystore fantongyo.keystore
/*解释：keytool工具是Java JDK自带的证书工具
-genkey参数表示：要生成一个证书（版权、身份识别的安全证书）
-alias参数表示：证书有别名，-alias fantongyo.keystore表示证书别名为:fantongyo
-keyalg RSA表示加密类型，RSA表示需要加密，以防止别人盗取
-validity 20000表示有效时间20000天( K3
-keystore fantongyo.keystore表示要生成的证书名称为fantongyo
*/

cd E:\SoftWare\adt-bundle-windows-x86-20140702\sdk\build-tools\android-4.4W