Работает, но не принимается валидатором как минимум по пунктам 3, 5

package com.javarush.task.task18.task1825;

import java.io.*;
import java.util.*;

public class Solution {
    public static void main(String[] args) {
        try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(System.in))) {
            Map<String, byte[]> partsWithData = new TreeMap<>();
            File joinedFile = null;
            FileOutputStream fileOutputStream = null;
            while (true) {
                String fileName = bufferedReader.readLine();
                if (fileName.equals("end")) break;
                FileInputStream fileInputStream = new FileInputStream(fileName);
                if (joinedFile == null) {
                    String[] joinedFileNames = fileName.split("\\.(?=[^\\.]+$)");
                    String joinFileName = joinedFileNames[0];
                    joinedFile = new File(joinFileName);
                    joinedFile.getParentFile().mkdirs();
                    joinedFile.createNewFile();
                    fileOutputStream = new FileOutputStream(joinedFile, true);
                }

                if (fileInputStream.available() > 0) {
                    byte[] bytesFromPart = new byte[fileInputStream.available()];
                    fileInputStream.read(bytesFromPart);
                    partsWithData.put(fileName, bytesFromPart);
                }
                fileInputStream.close();
            }

                for (Map.Entry<String, byte[]> entry: partsWithData.entrySet()) {
                    fileOutputStream.write(entry.getValue());
                }
               if (fileOutputStream != null) fileOutputStream.close();


        } catch (IOException e) {
            e.printStackTrace();

        }
    }
}

package com.javarush.task.task18.task1825;

import java.io.*;
import java.util.*;


public class Solution {
    public static void main(String[] args) {
        try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(System.in))) {
            Map<Integer, byte[]> partsWithData = new TreeMap<>();
            File joinedFile = null;
            FileOutputStream fileOutputStream = null;
            while (true) {
                String[] joinedFileNames = null;
                String fileName = bufferedReader.readLine();
                if (fileName.equals("end")) break;
                FileInputStream fileInputStream = new FileInputStream(fileName);
                joinedFileNames = fileName.split("\\.(?=[^\\.]+$)");
                if (joinedFile == null) {
                    String joinFileName = joinedFileNames[0];
                    joinedFile = new File(joinFileName);
                    joinedFile.getParentFile().mkdirs();
                    joinedFile.createNewFile();
                    fileOutputStream = new FileOutputStream(joinedFile, true);
                }

                if (fileInputStream.available() > 0) {
                    byte[] bytesFromPart = new byte[fileInputStream.available()];
                    fileInputStream.read(bytesFromPart);
                    partsWithData.put(Integer.parseInt(joinedFileNames[1].split("part")[1]), bytesFromPart);
                }
                fileInputStream.close();
            }

                for (Map.Entry<Integer, byte[]> entry: partsWithData.entrySet()) {
                    fileOutputStream.write(entry.getValue());
                }
                if (fileOutputStream != null) fileOutputStream.close();

        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

...
                mergedFile.getParentFile().mkdirs();
 ...

mergedFile.getParentFile().mkdirs();