I'm using wp_enqueue rather than including in the footer directly. I found that the path for the js files is correct (checked via page source).
NOT WORKING
wp_enqueue_script( 'jquery', get_template_directory_uri() . '/js/vendor/jquery.js', array (), NULL, true);
wp_enqueue_script( 'input', get_template_directory_uri() . '/js/vendor/what-input.js', array ('jquery'), NULL, true);
wp_enqueue_script( 'foundation-core', get_template_directory_uri() . '/js/vendor/foundation.js', array ('jquery'), NULL, true);
wp_enqueue_script( 'ext', get_template_directory_uri() . '/js/app.js', array ('jquery'), NULL, true);
WORKING
<script src="<?php bloginfo('template_directory'); ?>/js/vendor/jquery.js"></script>
<script src="<?php bloginfo('template_directory'); ?>/js/vendor/what-input.js"></script>
<script src="<?php bloginfo('template_directory'); ?>/js/vendor/foundation.js"></script>
<script src="<?php bloginfo('template_directory'); ?>/js/app.js"></script>