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Zend_Application should be able to configure the autoloader.
Posted by Matthew Weier O'Phinney (matthew) on 2009-04-17T06:10:46.000+0000
Currently, it allows you to pass an array of autoloader namespaces (via the 'autoloaderNamespaces' key). If you need more customization than that, it is recommended to either pull the autoloader from Zend_Application prior to calling bootstrap(), or to configure the autoloader prior to initializing Zend_Application.