Well remember the links defined for clicking anything in the application is determined by the settings in the admin panel. The application is always going to go to our scripts. If your doing something different in your modifications you would need to continue those modifications.. Our application would be run from this directory and you can mask things however you want but thats how it works.
LiveFolio - community photo gallery - LiveFolio
As I stated where we generate the thumbnails and there links are in our global file pp-inc.php in the function get_imagethumb and get_thumbtmpl
For the link you need to modify the later function.