Don't use the PHP Refactoring Plugin. It's never gotten out of alpha, there is no release to download and the only access to it is through it's subversion repository. And there are no commits the repository in a while, so the project is essentially dead.
There is some minimal refactoring support in Netbeans:
Rename Refactoring You can rename an element such as a class name across all files in a project. The feature forces you to preview your changes before you can make them. The preview window shows you every location of the element and lets you exclude individual occurrences of the element from being renamed. Rename Refactoring is contrasted with the older feature, Instant Rename, which lets you only rename an element within a file and which does not provide a preview window.
And Netbeans is as good a choice for a PHP IDE as any. PHPStorm also supports some refactoring functionality:
The Rename refactoring works for files, functions, constants, classes, properties, methods, parameters, and local and global variables.
Also following refactorings are available:
Introduce Variable
Introduce Constant
Introduce Field
Inline variable
Make global project changes easily and safely. Local changes are made instantly in-place.
But PHPStorm is not free.
There are quite a few non IDE refactoring tools for PHP in this related question.