Чего хочет, шайтан?
public static void main(String[] args) throws IOException {

        TreeMap<Integer, String> treeMap = new TreeMap<>();
        BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
        String file;
        while(!(file = reader.readLine()).equals("end")) {
            treeMap.put(Integer.parseInt(file.substring(file.indexOf(".part") + 5)), file);
        }
        reader.close();
        file = treeMap.firstEntry().getValue();

        File f = new File(file.substring(0, file.lastIndexOf(".")));

        FileOutputStream outputStream = new FileOutputStream(f);
        FileInputStream inputStream = null;

        for (Map.Entry<Integer, String> g : treeMap.entrySet()) {

            inputStream = new FileInputStream(g.getValue());
            byte[] buffer = new byte[inputStream.available()];
            inputStream.read(buffer);
            outputStream.write(buffer);
            inputStream.close();
        }
        outputStream.close();

    }

}