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With the default project structure set up, you have to decide how to manage the ZF Libraries.
As I'm only developing the structure for a single website and not developing an Enterprise Level web application, it makes more sense for me to go for option 2 and bundle the ZF Libraries within my project. I'm not expecting to offer the website for download as a commercial or open-source project, so the extra files from the ZF Libraries makes no difference to me in this case.
This is as simple as copying the library folder from the ZendFramework folder into your application's library folder.
In my case, I copied: