I am using the CI default .htaccess and the CI dynamic base_url().
My issue is that I have the deploy.php in the controllers folder but when I try and access via www.domain.com/deploy.php I get 404 not found why?
Codeigniter controllers are accessed like that www.domain.com/deploy(by class name in lower case, file name must match classname inside in lower case and class must extend CI_Controller)
The file you mention is nothing like that, so it is better to be called from the folder where index.php resides.