Various bits of PHP / HTML to customize this theme.

HTML

1. Change the manual slider to an auto transition slider

In custom.php add:

add_action('wp_footer', 'custom_slider_options');
function custom_slider_options() {
        ?>
        <script type="text/javascript">
            jQuery(window).load(function() {
                jQuery('.featured-slider .flexslider').flexslider({
                    slideshow: true,
                    slideshowSpeed: 1000
                });
            });
        </script>
        <?php
}

Where 1000 in the above sample would mean have 1 second between loading the next slide.

2. Remove mobile menu and use regular menu always

In custom.php add:

function mmenu_dequeue_script() {
    wp_dequeue_script('mmenu');
}
add_action( 'wp_print_scripts', 'mmenu_dequeue_script', 100 );

and in your Thesis Custom CSS add:

.toggle-menu {display: none !important;}
.nav-primary {display: inline !important;}