Try Inclued, a PECL package that extends PHP and reports file inclusions and other information. The manual introduction says:
Traces through and dumps the hierarchy of file inclusions and class inheritance at runtime. The files may have been included using include(), include_once(), require(), or require_once(). Class inheritance dependencies are also reported.
Also check out PHP_Depend, a code metrics tool for PHP. This does not exactly show file dependencies, but it reports code complexity metrics that may be of help as you're maintaining and refactoring an inherited PHP project.