How can I include the js and css file of my custom theme dynamically in header.php

I guess you wanted to enqueue all the files in your css and js directory of your theme. Thats the reason you are trying to use the scandir(). get_template_directory_uri() returns URL not the directory path. You need to use get_template_directory() for directory.

If you wanted to do that, then do it in functions.php

function enqueue_all_front_resources(){

   $js_directory = get_template_directory().'/js/';
   $all_js_files = array_diff(scandir($js_directory), array('..', '.'));
   // to avoid .. and . from the scandir function i used array_diff

   //now add the js with wp_enqueue_script()
   foreach($all_js_files as $js_file){
     wp_enqueue_script( $js_file.'-name', get_template_directory_uri() . '/js/'.$js_file );
   }


   $css_directory = get_template_directory().'/css/';
   $all_css_files = array_diff(scandir($css_directory), array('..', '.'));

   //now add the css with wp_enqueue_style()
   foreach($all_css_files as $css_file){
     wp_enqueue_style( $css_file.'-name', get_stylesheet_uri().'/css/'.$css_file );
   }

}

add_action('wp_enqueue_scripts','enqueue_all_front_resources');

Disadvantages in Doing this

• Unwanted resources will be added thus eats server as well browser(many file request and processing all scripts in browser makes little slow)
• You can’t give dependency correctly unless you name the js file with dependecy at the end of file name and parse add the dependency in enqueue_scripts and you need to take care of sorting too.

I Won’t recommand this method. I answered this for the interest of automation. Since you are thinking the dynamic way. Dynamic is good but we needs to be sure that it will work correctly and efficiently.