Magento is a beast of an eCommerce platform. It has a rigid set of conventions for the location and name of your theme files. And your theme should never overwrite any of the base installation that Magento creates. So how does a developer avoid the temptation to cut corners and “fix” things by hacking around with the Core?
Simple. Change the owner of the files to the web server user and don’t give write permissions to the user you are editing the files as. Then set Read/Write permission on just your theme folders.
sudo chown -R www:www /path-to-site/
sudo chmod -Rf 777 /path-to-site/app/design/frontend/themename /path-to-site/frontend/skin/themename/
Everytime you try to hack one of the core files, you’ll be denied…