How to implement a JavaScript and CSS file for my WordPress homepage?

You would enqueue it, this is how Javascript is added to WordPress properly. This function would typically go in your theme’s functions.php or in a plugin.

function my_scripts_intro() {
     is_front_page(){
         wp_enqueue_script( 'introjs','path to ..intro.js' );
         wp_enqueue_style( 'introcss','path to ..intro.css' );
        }
}

add_action( 'wp_enqueue_scripts', 'my_scripts_intro' );

To determine the state of the visitor you would probably want to use cookies.

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