Maybe what you're looking for is the resource loader.
http://framework.zend.com/manual/en/zend.loader.autoloader-resource.html
It lets you specify a path for a particular namespace.
Eg. you might have the following layout:
/application
/model
Using the resource loader you can set it up so that
My\Model\User.php => /application/model/User.php
Cheers,
David
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