If you're using the subversion checkouts of the Zend Framework, Matthew Weier O'Phinney recommends you update your checked out copy to bring it up to sync with the reorganization they've just finished.
We just completed a reorganization of our subversion repository. The reorganization was necessary due to changes we are introducting both in our proposal system as well as project architecture. Specifically, we are introducing a new library, our 'Extras' library, which will contain contributions that are not officially supported by Zend but which still require successful completion of our proposal process. Additionally, we are merging our Laboratory repository.
This page on the Zend Framework website gives the new structure along with a list of key changes and an example of how to switch our your current checkout with this new version.