If your question is about having WordPress CMS menus appear correctly, your code would be edited as follows:
<div class="collapse navbar-collapse nav-wil" id="bs-example-navbar-collapse-1">
<div class="top-menu">
<nav class="menu menu--francisco">
<div class="collapse navbar-collapse" id="navbar-menu">
<?php
$defaults = array(
'theme_location' => 'top',
'container' => '',
'menu_class' => 'nav navbar-nav menu__list',
'menu' => 'Header Menu'
);
wp_nav_menu($defaults); ?>
</div>
</nav>
</div>
</div>
Assuming register_nav_menu was used to register a “top” location, this will display the Header Menu in that location.
Your code displays both static HTML and commented out PHP, however. I may have completely misunderstood your question. Please rephrase it or add more information if so.
Full documentation on WordPress menu usage can be found in the Codex:
wp_nav_menu():
https://developer.wordpress.org/reference/functions/wp_nav_menu/
register_nav_menu():
https://developer.wordpress.org/reference/functions/register_nav_menu/