Where to call add_shortcode function in WordPress Plugin Boilerplate?

If you look at the /includes/class-plugin-loader.php you will see the

public function add_shortcode( $tag, $component, $callback, $priority = 10, $accepted_args = 2 ) {
        $this->shortcodes = $this->add( $this->shortcodes, $tag, $component, $callback, $priority, $accepted_args );
}

That builds a list of shortcodes to be registered with WordPress.
You use that via /includes/class-plugin.php within this function:

/**
 * Register all of the hooks related to the public-facing functionality
 * of the plugin.
 *
 * @since    1.0.0
 * @access   private
 */
private function define_public_hooks() {

    $plugin_public = new Plugin_Public( $this->get_plugin_name(), $this->get_version() );

    $this->loader->add_action( 'wp_enqueue_scripts', $plugin_public, 'enqueue_styles' );
    $this->loader->add_action( 'wp_enqueue_scripts', $plugin_public, 'enqueue_scripts' );

    $this->loader->add_shortcode( 'YOUR-SHORTCODE-NAME', $plugin_public, 'YOUR_CALLBACK_FUNCTION' );

}

For your callback function add it in the /public/class-plugin-public.php like this:

public function YOUR_CALLBACK_FUNCTION( $atts ){ 
    // do your shortcode stuff
}

Change plugin in the filenames above with your own plugin name.