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I'm trying to concoct a way to grab two (nearly identical) directories and show me the difference between all files in the two directories.

Looking for two different things:

1- List all files (recursively) that are different between the two directories

2- Subtract all the files in /new-directory/ from /old-directory/ and output the results to a third directory or someplace where I can easily scan over the differences.

I'm looking for backdoors to a server by comparing a backed up (clean) directory to one with a suspected backdoor (inside a a previously existing file).

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up vote 1 down vote accepted

If your goal is to compare the files, you can use diff directly, for example in that way:

diff -r old-dir new-dir

With an option -q you can suppress the differences and get only a list which files differ, or if some files exist only in one of those directories.

$ diff -r old-dir new-dir
Only in old-dir: 2
diff -r old-dir/3 new-dir/3
> this line was inserted by an evil hacker... 

$ diff -rq old-dir new-dir
Only in old-dir: 2
Files old-dir/3 and new-dir/3 differ

There is also a graphical interface, called xxdiff which facilitate the screening of the differences; Screenshot taken from homepage:

enter image description here

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Thanks! That's just what I was looking for. I didn't know if diff worked on a directory level. – Orun Bhuiyan Mar 4 '13 at 20:50
@OrunBhuiyan: Glad I could help. Btw. I think its uncommon here to thank "personally", just upvote and/or accept the answer -- and welcome to Superuser :) – mpy Mar 4 '13 at 20:53

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