Not sure if I completely follow you, but I think you want to avoid changing the "common" files if at all possible. With classes, this can be rather simplified by extending one of the common classes in a local class where you need some specific change for it to work in that one application. Then that application instantiates the child class instead of the parent (common) class. (So, your local class definition would require() the common class file, then extend it and override methods as needed to handle the specific requirements of your site-specific code.)
Or am I missing your point entirely?
My problem is I got classes that I want to use in my different websites. Lets assume I have a class called "CreateTable" in a file called "CreateTable.php". Other then adding new features to that class, or possible fixing small random bugs that would never break anything, I do not edit it. But if I do edit it, id want every single one of my projects with that class to have the latest versuin. I do not want to copy/past the "CreateTable.php" into each project, as this would turn into a mess each time I fixed a potential bug and/or added more functionality to that class.
My solution to this has been to use include_path in PHP.INI, so every single website has access to the folder that contains "CreateTable.php". What im asking is, if that is the way to go about this? I just want to be able to 'include' classes/functions into any website without having to copy/paste (duplicate) the PHP files.