What about using a version-control system?

Check your web directory into, say, CVS. CVS can then tell you if there are any files in your directory that are not in CVS (newly created) or which have contents different from those in CVS (modified). Doing this has the added advantage that you can quickly and easily restore the canonical version, and you can easily find out exactly what changed.

If CVS is the version system you choose, it can be handled very perlishly: there are a number of Cvs modules to use.