You are just printing out the result, so as it runs through the loop, it will print it all out on one line.
You could store the results in a separate array, or you could just do this to have them each print on a different line:
for (int i = 0; i < args.length; i++) {
BufferedReader reader = new BufferedReader (new FileReader (args[i]));
List<String> foo = simplify(reader);
for (int j = 0; j < foo.size(); j++) {
System.out.print(foo.get(j));
}
System.out.println();
}
The new println will separate each entry.