在@ Damien.Bell的请求下，以下示例涵盖了第一步和第二步：

    //These will be used as the source of the configuration file's stored attributes.
    private static final Map<String, String> COMMON_ATTRIBUTES = new HashMap<String, String>();
    private static final Map<String, char[]> SECURE_ATTRIBUTES = new HashMap<String, char[]>();
    //Ciphering (encryption and decryption) password/key.
    private static final char[] PASSWORD = "Unauthorized_Personel_Is_Unauthorized".toCharArray();
    //Cipher salt.
    private static final byte[] SALT = {
        (byte) 0xde, (byte) 0x33, (byte) 0x10, (byte) 0x12,
        (byte) 0xde, (byte) 0x33, (byte) 0x10, (byte) 0x12,};
    //Desktop dir:
    private static final File DESKTOP = new File(System.getProperty("user.home") + "/Desktop");
    //File names:
    private static final String NO_ENCRYPTION = "no_layers.txt";
    private static final String SINGLE_LAYER = "single_layer.txt";
    private static final String DOUBLE_LAYER = "double_layer.txt";

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws GeneralSecurityException, FileNotFoundException, IOException {
        //Set common attributes.
        COMMON_ATTRIBUTES.put("Gender", "Male");
        COMMON_ATTRIBUTES.put("Age", "21");
        COMMON_ATTRIBUTES.put("Name", "Hypot Hetical");
        COMMON_ATTRIBUTES.put("Nickname", "HH");

        /*
         * Set secure attributes.
         * NOTE: Ignore the use of Strings here, it's being used for convenience only.
         * In real implementations, JPasswordField.getPassword() would send the arrays directly.
         */
        SECURE_ATTRIBUTES.put("Username", "Hypothetical".toCharArray());
        SECURE_ATTRIBUTES.put("Password", "LetMePass_Word".toCharArray());

        /*
         * For demosntration purposes, I make the three encryption layer-levels I mention.
         * To leave no doubt the code works, I use real file IO.
         */
        //File without encryption.
        create_EncryptedFile(NO_ENCRYPTION, COMMON_ATTRIBUTES, SECURE_ATTRIBUTES, 0);
        //File with encryption to secure attributes only.
        create_EncryptedFile(SINGLE_LAYER, COMMON_ATTRIBUTES, SECURE_ATTRIBUTES, 1);
        //File completely encrypted, including re-encryption of secure attributes.
        create_EncryptedFile(DOUBLE_LAYER, COMMON_ATTRIBUTES, SECURE_ATTRIBUTES, 2);

        /*
         * Show contents of all three encryption levels, from file.
         */
        System.out.println("NO ENCRYPTION: \n" + readFile_NoDecryption(NO_ENCRYPTION) + "\n\n\n");
        System.out.println("SINGLE LAYER ENCRYPTION: \n" + readFile_NoDecryption(SINGLE_LAYER) + "\n\n\n");
        System.out.println("DOUBLE LAYER ENCRYPTION: \n" + readFile_NoDecryption(DOUBLE_LAYER) + "\n\n\n");

        /*
         * Decryption is demonstrated with the Double-Layer encryption file.
         */
        //Descrypt first layer. (file content) (REMEMBER: Layers are in reverse order from writing).
        String decryptedContent = readFile_ApplyDecryption(DOUBLE_LAYER);
        System.out.println("READ: [first layer decrypted]\n" + decryptedContent + "\n\n\n");
        //Decrypt second layer (secure data).
        for (String line : decryptedContent.split("\n")) {
            String[] pair = line.split(": ", 2);
            if (pair[0].equalsIgnoreCase("Username") || pair[0].equalsIgnoreCase("Password")) {
                System.out.println("Decrypted: " + pair[0] + ": " + decrypt(pair[1]));
            }
        }
    }

    private static String encrypt(byte[] property) throws GeneralSecurityException {
        SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
        SecretKey key = keyFactory.generateSecret(new PBEKeySpec(PASSWORD));
        Cipher pbeCipher = Cipher.getInstance("PBEWithMD5AndDES");
        pbeCipher.init(Cipher.ENCRYPT_MODE, key, new PBEParameterSpec(SALT, 20));

        //Encrypt and save to temporary storage.
        String encrypted = Base64.encodeBytes(pbeCipher.doFinal(property));

        //Cleanup data-sources - Leave no traces behind.
        for (int i = 0; i < property.length; i++) {
            property[i] = 0;
        }
        property = null;
        System.gc();

        //Return encryption result.
        return encrypted;
    }

    private static String encrypt(char[] property) throws GeneralSecurityException {
        //Prepare and encrypt.
        byte[] bytes = new byte[property.length];
        for (int i = 0; i < property.length; i++) {
            bytes[i] = (byte) property[i];
        }
        String encrypted = encrypt(bytes);

        /*
         * Cleanup property here. (child data-source 'bytes' is cleaned inside 'encrypt(byte[])').
         * It's not being done because the sources are being used multiple times for the different layer samples.
         */
//      for (int i = 0; i < property.length; i++) { //cleanup allocated data.
//          property[i] = 0;
//      }
//      property = null; //de-allocate data (set for GC).
//      System.gc(); //Attempt triggering garbage-collection.

        return encrypted;
    }

    private static String encrypt(String property) throws GeneralSecurityException {
        String encrypted = encrypt(property.getBytes());
        /*
         * Strings can't really have their allocated data cleaned before CG,
         * that's why secure data should be handled with char[] or byte[].
         * Still, don't forget to set for GC, even for data of sesser importancy;
         * You are making everything safer still, and freeing up memory as bonus.
         */
        property = null;
        return encrypted;
    }

    private static String decrypt(String property) throws GeneralSecurityException, IOException {
        SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
        SecretKey key = keyFactory.generateSecret(new PBEKeySpec(PASSWORD));
        Cipher pbeCipher = Cipher.getInstance("PBEWithMD5AndDES");
        pbeCipher.init(Cipher.DECRYPT_MODE, key, new PBEParameterSpec(SALT, 20));
        return new String(pbeCipher.doFinal(Base64.decode(property)));
    }

    private static void create_EncryptedFile(
                    String fileName,
                    Map<String, String> commonAttributes,
                    Map<String, char[]> secureAttributes,
                    int layers)
                    throws GeneralSecurityException, FileNotFoundException, IOException {
        StringBuilder sb = new StringBuilder();
        for (String k : commonAttributes.keySet()) {
            sb.append(k).append(": ").append(commonAttributes.get(k)).append(System.lineSeparator());
        }
        //First encryption layer. Encrypts secure attribute values only.
        for (String k : secureAttributes.keySet()) {
            String encryptedValue;
            if (layers >= 1) {
                encryptedValue = encrypt(secureAttributes.get(k));
            } else {
                encryptedValue = new String(secureAttributes.get(k));
            }
            sb.append(k).append(": ").append(encryptedValue).append(System.lineSeparator());
        }

        //Prepare file and file-writing process.
        File f = new File(DESKTOP, fileName);
        if (!f.getParentFile().exists()) {
            f.getParentFile().mkdirs();
        } else if (f.exists()) {
            f.delete();
        }
        BufferedWriter bw = new BufferedWriter(new FileWriter(f));
        //Second encryption layer. Encrypts whole file content including previously encrypted stuff.
        if (layers >= 2) {
            bw.append(encrypt(sb.toString().trim()));
        } else {
            bw.append(sb.toString().trim());
        }
        bw.flush();
        bw.close();
    }

    private static String readFile_NoDecryption(String fileName) throws FileNotFoundException, IOException, GeneralSecurityException {
        File f = new File(DESKTOP, fileName);
        BufferedReader br = new BufferedReader(new FileReader(f));
        StringBuilder sb = new StringBuilder();
        while (br.ready()) {
            sb.append(br.readLine()).append(System.lineSeparator());
        }
        return sb.toString();
    }

    private static String readFile_ApplyDecryption(String fileName) throws FileNotFoundException, IOException, GeneralSecurityException {
        File f = new File(DESKTOP, fileName);
        BufferedReader br = new BufferedReader(new FileReader(f));
        StringBuilder sb = new StringBuilder();
        while (br.ready()) {
            sb.append(br.readLine()).append(System.lineSeparator());
        }
        return decrypt(sb.toString());
    }

一个解决每个保护步骤的完整示例将远远超出我认为对该问题的合理范围，因为它是关于“步骤是什么”而不是“如何应用它们”。

这将大大超出我的答案的大小（最后是抽样），而SO上的其他问题已经针对这些步骤的“如何进行”，更加合适，并且为实施这些问题提供了更好的解释和抽样。每个步骤。