If you want to change the path of magento core application folder, then you can set it as:
Mage::setRoot('/path/to/your/app');
If you look into app/Mage.php you will find that function.
/** * Set application root absolute path * * @param string $appRoot * @throws Mage_Core_Exception */ public static function setRoot($appRoot = '') { if (self::$_appRoot) { return ; } if ('' === $appRoot) { // automagically find application root by dirname of Mage.php $appRoot = dirname(__FILE__); } $appRoot = realpath($appRoot); if (is_dir($appRoot) and is_readable($appRoot)) { self::$_appRoot = $appRoot; } else { self::throwException($appRoot . ' is not a directory or not readable by this user'); } }