WP - Ensure custom post types work with category and tag searches

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add_filter('pre_get_posts', 'query_post_type');
function query_post_type($query) {
  if(is_category() || is_tag()) {
    $post_type = get_query_var('post_type');
	if($post_type)
	    $post_type = $post_type;
	else
	    $post_type = array('post','cpt'); // replace cpt to your custom post type
    $query->set('post_type',$post_type);
	return $query;
    }
}

// source: http://wordpress.org/support/topic/custom-post-type-tagscategories-archive-page