Encoder

    public static String encode(String message){

        System.out.println("DECODED: " + message);

        char[] alphabet = "abcdefghijklmnopqrstuvwxyz".toCharArray();

        for(int i = 0; i < alphabet.length; i++){
            message = message.replace(Character.toString(alphabet[i]), KeyGenerator.order.get(i));
        }

        System.out.println("ENCODED: " + message);

        message = Base64.getEncoder().encodeToString(message.getBytes());

        System.out.println("BASE64 ENCODED: " + message);

        return message;
    }

Decoder

public static String decode(String message){

        System.out.println("BASE64 ENCODED: " + message);

        message = new String(Base64.getDecoder().decode(message.getBytes()));

        System.out.println("BASE64 DECODED: " + message);

        char[] alphabetChars = "abcdefghijklmnopqrstuvwxyz".toCharArray();

        for(int i = 0; i < alphabetChars.length; i++){
            alphabet.add(Character.toString(alphabetChars[i]));
        }

        int loopsize = alphabet.size();

        for(int i = 0; i < loopsize; i++){
            message = message.replace(KeyGenerator.order.get(i), alphabet.get(i));
            alphabet.remove(i);
            KeyGenerator.order.remove(i);
            System.out.println(KeyGenerator.order.get(i) + " | " + alphabet.get(i) + " | " + message);
        }

        System.out.println("DECODED: " + message);

        return message;
    }

WHY THE FUCK DOESN"T THE DECODER WORK

Key: gzsndpkwfbjaemhrqicutlyvxo
DECODED: This message is a test
ENCODED: Txfc edccjjd fc j tdct
BASE64 ENCODED: VHhmYyBlZGNjampkIGZjIGogdGRjdA==
BASE64 ENCODED: VHhmYyBlZGNjampkIGZjIGogdGRjdA==
BASE64 DECODED: Txfc edccjjd fc j tdct
z | b | Txfc edccjjd fc j tdct
n | d | Txfc edccjjd fc j tdct
p | f | Txfc eeccjje fc j tect
w | h | Txfc eeccjje fc j tect
b | j | Txic eeccjje ic j tect
a | l | Txic eecckke ic k tect
m | n | Txic mmcckkm ic k tmct
r | p | Txic mmcckkm ic k tmct
i | r | Txic mmcckkm ic k tmct
u | t | Txis mmsskkm is k tmst
l | v | Txis mmsskkm is k umsu
v | x | Txis mmsskkm is k umsu
o | z | Tyis mmsskkm is k umsu
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 13, Size: 13
	at java.util.LinkedList.checkElementIndex(LinkedList.java:555)
	at java.util.LinkedList.get(LinkedList.java:476)
	at Decoder.decode(Decoder.java:30)
	at Main.main(Main.java:12)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:483)
	at com.intellij.rt.execution.application.AppMain.main(AppMain.java:140)