Let's say you've got an older PHP application. Once upon a time, it was wired together by a pile of includes with no real organization or planning behind the organization. A developer went through and cleaned up the file organization.

That's a happy ending, isn't it? No, it isn't, not for Scott. Because the developer doing the cleanup didn't want to risk breaking any files, and thus didn't actually do any final cleanup. Instead, in the labirynth of a thousand include files, many of them are dead ends containing only:

<?php
//Old file, linked in all over the place.  not used anymore.
?>
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