В чём беда?
package com.javarush.task.task19.task1925;
import java.io.*;
import java.util.ArrayList;
/*
Длинные слова
*/
public class Solution {
public static void main(String[] args) throws Exception{
BufferedReader reader = new BufferedReader(new FileReader(args[0]));
// BufferedWriter writer = new BufferedWriter(new FileWriter(args[1]));
FileWriter fileWriter = new FileWriter(args[1]);
while (reader.ready()){
String [] s = reader.readLine().split(" ");
String s1 = "";
for(int i = 0; i < s.length; i++) {
if (s[i].length() > 6) {
//writer.write(s[i]);
s1 += s[i];
if (!(i+1 == s.length)){
s1 += ",";
}
}
}
if(reader.ready()) {
s1+=",";
}
fileWriter.write(s1);
}
reader.close();
//writer.close();
fileWriter.close();
}
}