If you want to link stylesheets and scripts in wordpress,the correct way is to use wp_enqueue_style() and wp_enqueue_scripts() in your functions.php file
Try this in your functions.php file
wp_enqueue_style('bootstrap-css',get_template_directory_uri()."https://wordpress.stackexchange.com/bootstrap/css/bootstrap.min.css");
wp_enqueue_script('jquery',get_template_directory_uri().'/scripts/jquery.min.js');
wp_enqueue_script('bootstrap-js',get_template_directory_uri().'/bootstrap/js/bootstrap.min.js');