Want to add my custom prepare query but add_filter doesn’t run

I want to manipulate the order of WP_User_Query(). I want the user to come out ordered by a custom meta field and by ascending order.

I have the code correctly working tested it on users.php but since this is not a good place to put it I wanted to run add_filter( 'prepare_query', 'my_prepare_query');

The call in the theme (‘include’ doesn’t exist):

$count_args = array(
    'include' => $include,
    'number' => 999999,
    'fields' => 'ID',
    'orderby' => 'include',
    'order' => 'ASC'
);
$user_count_query = new WP_User_Query( $count_args );

I just simply added another elseif to prepare_query on line 433 of user.php:

elseif ( 'include' == $qv[ 'orderby' ] ) {

    $this->query_from .= " INNER JOIN wp_usermeta ON wp_usermeta.user_id = $wpdb->users.ID";
    $this->query_where .= " AND wp_usermeta.meta_key = 'my_userpoints'";
    $orderby = "wp_usermeta.meta_value";
}

Now why is the add_filter not overwriting the user.php function? Is it not possible to overwrite core functions?

The WP_User_Query allows meta_query searches exactly like the other WP_*_Query classes. Example here:

global $wpdb;
$author_search = new WP_User_Query( array(
    'role'       => 'subscriber', 
    'fields'     => 'all_with_meta',
    // if it's a digit/int/float, use 'meta_value_num'
    'orderby'    => 'meta_value',
    'order'      => 'ASC',
    // you could try -1 as well.
    'nuber'      => 99999999,
    'meta_query' => array(
        'key'     => 'my_userpoints',
        // only needed if you got a specific value you search for
        // 'value'   => '',
        // only needed if you got a specific value you search for
        // and want to compare against it. For e.g. '>', '<', etc. See Codex.
        // 'compare' => '',
        'type'    => 'CHAR', // this is the default, use INT if you got an int/float value
    ),
) );
$author_list   = $author_search->get_results();
$author_count  = $wpdb->num_rows;