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<?php
require_once('app/Mage.php');
Mage::app();

$stores = array_map(function($store) {
    return $store->getId();
}, Mage::app()->getStores(true));

foreach ($stores as $store_id) {
    // Setup app emulation
    $appEmulation = Mage::getSingleton('core/app_emulation');
    $initialEnvironmentInfo = $appEmulation->startEnvironmentEmulation($store_id);

    // Load up an emulated category
    $cat = Mage::getModel('catalog/category')->load(3);

    // Output the URL
    echo $cat->getUrl() . PHP_EOL;

    // Turn off emulation
    $appEmulation->stopEnvironmentEmulation($initialEnvironmentInfo);
}