According to the Zend Developer Zone, the Zend Framework is going to the even more powerful in the future with the inclusion of command line functionality.

So, without further adieu, it is my pleasure to announce that Zend Framework 1.5 will include a robust, powerful, and- yes- 15-minute-demo-enabled command line interface for code generation!

They've set up a default structure (that's "recommended") but doesn't have to be strictly adhered to. They know how most developers have structured their applications and made it accordingly. There's three proposals in the group - the Zend_Console, Zend_Build component and the Zend_Build for Core.