The browser interprets your page as it loads so the script in your header executes immediately;
$('.menu-toggle').click(...)
however at this moment you haven't loaded the body of the page so there are no elements with the menu-toggle class to attach to.
You need to either attach your events on the dom ready event which ensures the js runs after everything has loaded
$( document ).ready() | jQuery Learning Center[
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or move your script to the bottom of the page so the elements exist when the code is ran.