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<?php
/** only use queries with facetwp=>true in its args
 ** this can be used with facetwp templates by adding facetwp=>true
 ** in all your template queries
 **/
add_filter( 'facetwp_is_main_query', function( $is_main_query, $query ) {
    if ( true !== $query->get( 'facetwp' ) ) {
        $is_main_query = false;
    }
    return $is_main_query;
}, 10, 2 );