Where these .js file come to source code?

they’re wp_enqueue_script() scripts.

You can remove them (if you’re positive nothing uses them) with wp_dequeue_script() similar to the following:

add_action( 'wp_enqueue_scripts', function() {
   wp_deregister_script( 'jquery' );
   wp_deregister_script( 'wp-embed' );
}, 99 );

or with

add_filter( 'wp_default_scripts', function(&$scripts){
    if(!is_admin()) {
        $scripts->remove( 'jquery' );
        $scripts->remove( 'wp-embed' );
    }
} );