PHP 5.5 has Opcache built-in. Opcache is supposed to invalidate when the script has changed, but it has issue when the script is in a symlinked folder and called from the webserver.
Basically, Opcache "thinks" that the script is /var/www/hello/current/public/index while in reality, it's /var/www/hello/releases/20140101011/public/index.
To solve the issue, add the following command to be run at the end of your deployment:
php -r "opcache_reset();"
Note: if you are using PHP-FPM with nginx, the above will only flush the CLI cache, not FPM's
To fix the problem in this case, add the lines below to your nginx server configuration.
fastcgi_param SCRIPT_FILENAME $realpath_root$fastcgi_script_name;
fastcgi_param DOCUMENT_ROOT $realpath_root;
Usually the file is located at /etc/nginx/fastcgi.conf.