You've got three folders:

  • folder current, which contains your current files
  • folder old, which contains an older version of the same files
  • folder difference, which is just an empty folder

How do you compare old with current and copy the files which are different (or entirely new) in current to difference?

I have searched all around and it seems like a simple thing to tackle, but I can't get it to work in my particular example. Most sources suggested the use of rsync so I ended up with the following command:

rsync -ac --compare-dest=../old/ new/ difference/

What this does however, is copies all the files from new to difference, even those which are the same as in old.

In case it helps (maybe the command is fine and the fault lies elsewhere), this is how I tested this:

  1. I made the three folders.
  2. I made several text files with different contents in old.
  3. I copied the files from old to new.
  4. I changed the contents of some of the files in new and added a few additional files.
  5. I ran the above command and checked the results in difference.

I have been looking for a solution for the past couple of days and I'd really appreciate some help. It doesn't necessarily have to be using rsync, but I'd like to know what I'm doing wrong if possible.

  • possible duplicate of How do I save changed files? Commented Dec 8, 2013 at 5:45
  • @wingedsubmariner I don't think it is a duplicate, as the accepted answer at the linked question, is the command that the OP is asking a question about.
    – Bernhard
    Commented Dec 8, 2013 at 18:20
  • @Bernhard Ah, my bad. I guess I misunderstood the original question. Commented Dec 8, 2013 at 18:58
  • @wingedsubmariner No worries, you said "possible", and I agree it looks very similar :)
    – Bernhard
    Commented Dec 8, 2013 at 20:52

5 Answers 5


I have figured out what the problem was in my case:

The files I was comparing had different timestamps. I shouldn't have used the -a argument, I assume because rsync was trying to preserve the timestamps when copying files. The command which worked for me was:

rsync -rvcm --compare-dest=../old/ new/ difference/
  • I think to test this with the -a (archive) option, you should have used rsync -a to "copy" the files initially (or the cp equivalent), then deleted or modified. (I like to stick to rsync because I know it is self-consistent without thinking about what it might be doing.) I think that should have worked with the original command. The -a option includes -t (compare by timestamp), which is the alternative to -c (compare by checksum).
    – sage
    Commented Sep 4, 2014 at 17:44
  • 2
    In my opinion, this answer should be the one accepted, as it's far more simple. Also, the command only worked for me when I provided the full path for old/ and new/.
    – Yamaneko
    Commented Nov 3, 2015 at 18:05
  • 2
    The caveat seems to be that the compare-dest must be the relative path to the difference as seen from inside the actual dest Commented May 8, 2019 at 1:20

I am not sure whether you can do it with any existing linux commands such as rsync or diff. But in my case I had to write my own script using Python, as python has the "filecmp" module for file comparison. I have posted the whole script and usage in my personal site - http://linuxfreelancer.com/

It usage is simple - give it the absolute path of new directory, old directory and difference directory in that order.

#!/usr/bin/env python

import os, sys
import filecmp
import re
from distutils import dir_util
import shutil

holderlist = []

def compareme(dir1, dir2):
    dircomp = filecmp.dircmp(dir1, dir2)
    only_in_one = dircomp.left_only
    diff_in_one = dircomp.diff_files
    dirpath = os.path.abspath(dir1)
    [holderlist.append(os.path.abspath(os.path.join(dir1, x))) for x in only_in_one]
    [holderlist.append(os.path.abspath(os.path.join(dir1, x))) for x in diff_in_one]
    if len(dircomp.common_dirs) > 0:
        for item in dircomp.common_dirs:
                os.path.abspath(os.path.join(dir1, item)),
                os.path.abspath(os.path.join(dir2, item)),
        return holderlist

def main():
    if len(sys.argv) > 3:
        dir1 = sys.argv[1]
        dir2 = sys.argv[2]
        dir3 = sys.argv[3]
        print "Usage: ", sys.argv[0], "currentdir olddir difference"

    if not dir3.endswith("/"):
        dir3 = dir3 + "/"

    source_files = compareme(dir1, dir2)
    dir1 = os.path.abspath(dir1)
    dir3 = os.path.abspath(dir3)
    destination_files = []
    new_dirs_create = []
    for item in source_files:
        destination_files.append(re.sub(dir1, dir3, item))
    for item in destination_files:
    for mydir in set(new_dirs_create):
        if not os.path.exists(mydir):
    # copy pair
    copy_pair = zip(source_files, destination_files)
    for item in copy_pair:
        if os.path.isfile(item[0]):
            shutil.copyfile(item[0], item[1])

if __name__ == "__main__":

This might help some readers: In Windows, an older, little freeware program -- Third Dir -- does exactly what's being asked for here. It's no longer available via the developer, Robert Vašíček. But I'm sure it can be found via some repositories online.

Here's the developer's description, which remains on his site:

Third Dir: An unusual directory-synchronizer - the different files are copied to third directory. It is very useful to extract e.g. new or edited photos from a huge directory tree on fixed disk to temporary folder, then add them to archive CD (note - the original files are compared against the CD). Version 1.4, size 23kB. Created 2005-02-12.

History: Version 1.14 - More efficient when many ten of thousands of files are compared.


The rsync way given by Thane with Yamaneko additions work great but leave empty directories. For me the final solution was in two steps, first call rsync with full path, then a find command to remove all empty directories:

rsync -rvcm --compare-dest=/tmp/org/ /tmp/new/ /tmp/difference/
find /tmp/difference/ -d -type d -empty -exec rmdir {} \; -print

Please note than even with --links option, rsync did not keep symbolic links but copied the destination data instead.

  • Note that instead of -empty -exec rmdir {} \; you can use -empty -delete.
    – mivk
    Commented Jul 2, 2019 at 10:24

I use the dualpane XY Explorer (commercial), which can do a lot of tricks and this is one of them. Open Current in one pane and Old in the other. Activate the Current pane. Go to Panes > Sync Select. It gives you 5 options to select:

  1. Matches (listed in both)
  2. Uniques (in the active pane)
  3. Newer (in the active pane)
  4. Unique and Newer files (in the active pane)
  5. Selected (those selected in the other pane)

Now you can copy the resulting selection from Current to where you want. I used it to compare mailfolders from old installs with the the latest. The folder structure was quite complex, but (almost) all mbs-files had a unique number.

So I did a search on mbs-files in the old root mailfolder (in one pane) as well as on the newest (in the other pane) and did a comparison on the search results in each pane (Sync Select Unique, to find mails that went missing during re-installs)! You can set a lot of options too.

  • 1
    If you are talking about non standard software, you should include a link. If you mean XYplorer that is not going to help the OP at all.
    – Anthon
    Commented Jan 24, 2014 at 13:23

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