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

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