A lot of core JavaScript files not being included
I figured out that using drupal_add_js outside of a hook_js_alter function in another file was causing the issue.

drupal_add_js($form_js, array('type' =&gt; 'inline', 'scope' =&gt; 'footer'));


Now that it is within the function, it's working fine.

I don't see anything in the documentation saying that this is required -> also, drupal_add_css works fine outside of a function. I'm not altering any existing JS files, only adding new ones.

So while I don't understand why this is an issue, this is the solution