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I would add some error checking. Ensuring that your mkdir was successful when creating your backup directory, and that your backups were created successfully are important. If you care enough to...

You didn't mention what OS you are on, the below cp options may or may not be available to you:

Consider preserving files mode,ownership,timestamps and context (via the cp -p and -c options).
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As mentioned in my post, error checking was omitted, and it was based on the assumption of files of equal length.
diff is great at finding missing lines: diff file1 file2
3c3
<...