cleanupPreferences.php

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<?php
require_once __DIR__ . '/Maintenance.php';

class CleanupPreferences extends Maintenance {
    public function execute() {
        global $wgHiddenPrefs;

        $dbw = wfGetDB( DB_MASTER );
        $dbw->begin( __METHOD__ );
        foreach ( $wgHiddenPrefs as $item ) {
            $dbw->delete(
                'user_properties',
                array( 'up_property' => $item ),
                __METHOD__
            );
        };
        $dbw->commit( __METHOD__ );
        $this->output( "Finished!\n" );
    }
}

$maintClass = 'CleanupPreferences'; // Tells it to run the class
require_once RUN_MAINTENANCE_IF_MAIN;