I have just had a big blitz on security on my main site. Some securtiy breaches can involve a hacker subtley adding or changing file on your server, resulting in an open back door. In a large site, this can be difficult to detect. The hackers sometimes make the filenames follow the same conventions as the other thousands of files in the site so they blend in.
I found a free tool which is great for this kind of work. You simply point it at the two sets of files that you want to compare, and it presents you with a list of pairs and results. You can then click on any pair of documents to analyse the differences.
WinMerge can be found at: http://winmerge.sourceforge.net/
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