I\'ve got a somewhat primitive framework I\'ve been using for most of my projects, but a general design issue came to mind that I haven\'t been able to work out yet. For a given
I would suggest that you view your source code in two different categories, external dependencies or code that is used across multiple sites and not native to any single one and native dependencies or the code that is native to the particular site that you're working on.
It sounds like Framework/Control.php is part of a larger external dependency and should be managed as such, while the Application/Control files are all native the particular website.
Using this differentiation in our code structure has made it much easier to reuse our in-house framework between multiple sites very easily.
As a final thought, you might consider looking at what the major frameworks out there are doing such as Zend Framework, Symfony and others. Even though the entire framework might be more than you want the structure of the frameworks can provide a lot of insights into common, good practices that are being used by PHP developers everywhere.