Сделал всё правильно.
package com.javarush.task.task18.task1825;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.Comparator;
import java.util.Set;
import java.util.TreeSet;
/*
Собираем файл
*/
public class Solution {
public static void main(String[] args) throws Exception {
TreeSet<String> names = new TreeSet<String>();
BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
String filename = "";
String file = "";
while (!((filename = reader.readLine()).equals("end")))
{
names.add(filename);
file = filename.substring(0, filename.lastIndexOf(".") - 1 );
}
FileOutputStream outputStream = new FileOutputStream(file, true);
for(String name : names)
{
FileInputStream inputStream = new FileInputStream(name);
byte[] buffer = new byte[inputStream.available()];
int count = inputStream.read(buffer);
outputStream.write(buffer);
inputStream.close();
}
outputStream.close();
}
}