The root of your application document is where you place the index.php file, the location of the Zend Framework library and the application code do not matter.
If you used the BaseUrl helper helper in your views for static assets (JavaScript, CSS, images) and the Url helper to reference actions, your application should be very portable regarding the relative path from the root of the web server document.
Let me know if I am leaving here. Your question may concern more details.
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