Вроде-бы правильно ...
package com.javarush.task.task18.task1826;
/*
Шифровка
*/
import java.io.*;
public class Solution {
public static void main(String[] args) throws IOException{
BufferedInputStream stream1 = new BufferedInputStream(new FileInputStream(args[1]));
BufferedOutputStream stream2 = new BufferedOutputStream(new FileOutputStream(args[2]));
byte [] bytes = new byte[args[1].length()];
stream1.read(bytes);
if (args[0].equals("-e")) {
byte[] result = java.util.Base64.getEncoder().encode(bytes);
stream2.write(result);
stream2.close();
}
else if (args[0].equals("-d")) {
byte[] result = java.util.Base64.getDecoder().decode(bytes);
stream2.write(result);
stream2.close();
}
stream1.close();
}
}