ArrayList<String> list1 = new ArrayList<String>();
        ArrayList<String> list2 = new ArrayList<String>();
        BufferedReader reader = new BufferedReader((new InputStreamReader(System.in)));
        BufferedReader fileReader1 = new BufferedReader(new FileReader(reader.readLine()));
        BufferedReader fileReader2 = new BufferedReader(new FileReader(reader.readLine()));
        reader.close();
        while(fileReader1.ready()) list1.add(fileReader1.readLine());
        fileReader1.close();
        while(fileReader2.ready()) list2.add(fileReader2.readLine());
        fileReader2.close();

        for(int i = 0; i < (list1.size() - 1); i++) {
            if (i == (list2.size()) - 1 && list1.get(i).equals(list2.get(i))) {
                lines.add(new LineItem(Type.SAME, list1.get(i)));
                lines.add(new LineItem(Type.REMOVED, list1.get(i + 1)));
                break;
            }

            else if (list2.get(i).equals(list1.get(i + 1))) {
                lines.add(new LineItem(Type.REMOVED, list1.get(i)));
                list2.add(i, "");
            } else if (list1.get(i).equals(list2.get(i + 1))) {
                lines.add(new LineItem(Type.ADDED, list2.get(i)));
                list1.add(i, "");
            } else if (list1.get(i).equals(list2.get(i))) {
                lines.add(new LineItem(Type.SAME, list1.get(i)));
            }
        }

        if(list2.size() == list1.size()) lines.add(new LineItem(Type.SAME, list1.get(list1.size() - 1)));
        else if(list2.size() > list1.size()) {
            lines.add(new LineItem(Type.SAME, list1.get(list1.size() - 1)));
            lines.add(new LineItem(Type.ADDED, list2.get(list2.size() - 1)));
        }

        for(LineItem t: lines) System.out.println(t.toString());

    }
Вариант вывода
SAME 1
REMOVED 2
SAME 3
REMOVED 4
SAME 5
ADDED 0
SAME 1
REMOVED 2
SAME 3
ADDED 4
SAME 5
REMOVED 0