import org.apache.commons.codec.digest.DigestUtils;

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

public String calcMD5HashForDir(File dirToHash, boolean includeHiddenFiles) {

    assert (dirToHash.isDirectory());
    Vector<FileInputStream> fileStreams = new Vector<FileInputStream>();

    System.out.println("Found files for hashing:");
    collectInputStreams(dirToHash, fileStreams, includeHiddenFiles);

    SequenceInputStream seqStream =
            new SequenceInputStream(fileStreams.elements());

    try {
        String md5Hash = DigestUtils.md5Hex(seqStream);
        seqStream.close();
        return md5Hash;
    }
    catch (IOException e) {
        throw new RuntimeException("Error reading files to hash in "
                                   + dirToHash.getAbsolutePath(), e);
    }

}

private void collectInputStreams(File dir,
                                 List<FileInputStream> foundStreams,
                                 boolean includeHiddenFiles) {

    File[] fileList = dir.listFiles();
    Arrays.sort(fileList,               // Need in reproducible order
                new Comparator<File>() {
                    public int compare(File f1, File f2) {
                        return f1.getName().compareTo(f2.getName());
                    }
                });

    for (File f : fileList) {
        if (!includeHiddenFiles && f.getName().startsWith(".")) {
            // Skip it
        }
        else if (f.isDirectory()) {
            collectInputStreams(f, foundStreams, includeHiddenFiles);
        }
        else {
            try {
                System.out.println("\t" + f.getAbsolutePath());
                foundStreams.add(new FileInputStream(f));
            }
            catch (FileNotFoundException e) {
                throw new AssertionError(e.getMessage()
                            + ": file should never not be found!");
            }
        }
    }

}