recalculateURIs.php

<?php
$modx = new modX();

$modx->setLogTarget(XPDO_CLI_MODE ? 'ECHO' : 'HTML');
$modx->initialize('mgr');
$modx->setLogLevel(modX::LOG_LEVEL_INFO);
$modx->exec("UPDATE {$modx->getTableName('modResource')} SET uri = '' WHERE uri_override = 0");

//$modx->call('modResource', 'refreshURIs', array(&$modx));
foreach ($modx->getIterator('modResource', $criteria) as $resource) {
    $resource->set('refreshURIs', true);
    if ($resetOverrides) {
        $resource->set('uri_override', false);
    }
    if (!$resource->get('uri_override')) {
        $resource->set('uri', '');
    }
    $resource->save();
}