The best solution for refactoring in PHP is engineered by Zend, the company behind PHP.
They offer an enterprise bundle of Eclipse PDT with a set of feature-rich proprietary Zend enhancements. It's marketed under the label "Zend Studio" and used by professional PHP developers.
Download a free trial and see how Zend Studio boosts your productivity. It has more relevant PHP features than any competitor, incl. out-of-the-box Team Collaboration (GIT, GitHub, SVN, CVS), integrated PHP and JavaScript debugging, profiling, code inspection & quick fix, test generation & reporting, and others.
For instance, see Zend Studio in comparison to Eclipse PDT Project.
I've been using the product for already 5 years to my full satisfaction. It is something to consider if you're after enterprise PHP development, or a beginning developer who wants to become a pro.
Refactoring in Zend Studio has exactly what you are asking for, i.e. when you rename a file, it scans all files for references, automatically proposes changes to the includes and then applies changes after your confirmation. In addition, I've observed many uses for the feature which takes you straight to the body of a function on CTRL+click. This is extremely useful when changing function names, variable names, and bodies. Zend Studio again scans all files, builds a cross-reference table, and does all changes for you.