Bootstrap subtheme does not apply to main menu After adding the "html.tpl.php" and "page.tpl.html" to my bootstrap subtheme the layout of my main menu disappeard as you can see in the screenshot below:



As you can see; no bootstrap classes are applied to the menu:

&lt;h2 class="block-title"&gt;Main menu&lt;/h2&gt;
    &lt;div class="contextual-links-wrapper"&gt;&lt;ul class="contextual-links"&gt;&lt;li class="menu-list first"&gt;&lt;a href="/drupal/admin/structure/menu/manage/main-menu/list?destination=node"&gt;List links&lt;/a&gt;&lt;/li&gt;
&lt;li class="menu-edit"&gt;&lt;a href="/drupal/admin/structure/menu/manage/main-menu/edit?destination=node"&gt;Edit menu&lt;/a&gt;&lt;/li&gt;
&lt;li class="block-configure last"&gt;&lt;a href="/drupal/admin/structure/block/manage/system/main-menu/configure?destination=node"&gt;Configure block&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;&lt;/div&gt;
  &lt;ul class="menu nav"&gt;&lt;li class="first leaf"&gt;&lt;a href="/drupal/lessenrooster"&gt;Lessenrooster&lt;/a&gt;&lt;/li&gt;
&lt;li class="collapsed"&gt;&lt;a href="/drupal/over-ons"&gt;Over ons&lt;/a&gt;&lt;/li&gt;
&lt;li class="leaf"&gt;&lt;a href="/drupal/contact" title=""&gt;Contact&lt;/a&gt;&lt;/li&gt;
&lt;li class="last leaf"&gt;&lt;a href="/drupal/fotogallerij"&gt;Fotogallerij&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;/section&gt;


The bootstrap subtheme however is active:



EDIT 1

I indeed did use the wrong .tpl files. I now have copied the correct files to the subtheme (which included the correct .info file). However the .info file does not include the main_menu region.

regions[navigation]     = 'Navigation'
regions[header]         = 'Top Bar'
regions[highlighted]    = 'Highlighted'
regions[help]           = 'Help'
regions[content]        = 'Content'
regions[sidebar_first]  = 'Primary'
regions[sidebar_second] = 'Secondary'
regions[footer]         = 'Footer'
regions[page_top]       = 'Page top'
regions[page_bottom]    = 'Page bottom'


After clearing the cache, the main menu did not change.

EDIT 2

I started all over again following this guide, but still the main menu looks like crap... and if i copy over the menu folder from bootstrap I get an HTTP ERROR 500 error
You must use the template files from bootstrap theme since all those are overridden there. the templates file you should use are under themes &gt; bootstrap &gt; templates &gt; system. 

copy the page.tpl.php and html.tpl.php from there to your sub-theme.

simply use the same .info file for your sub theme as well. it will give you all the regions. set "base theme=bootstrap" in template_name.info file.

remember to clear the cache