custom.js

$(function() {

  // Automatically scroll the navigation menu to the active element
  //   https://github.com/civicrm/civicrm-dev-docs/issues/21
  $.fn.isFullyWithinViewport = function(){
      var viewport = {};
      viewport.top = $(window).scrollTop();
      viewport.bottom = viewport.top + $(window).height();
      var bounds = {};
      bounds.top = this.offset().top;
      bounds.bottom = bounds.top + this.outerHeight();
      return ( ! (
        (bounds.top <= viewport.top) ||
        (bounds.bottom >= viewport.bottom)
      ) );
  };
  if( !$('li.toctree-l1.current').isFullyWithinViewport() ) {
    $('.wy-nav-side')
      .scrollTop(
        $('li.toctree-l1.current').offset().top -
        $('.wy-nav-side').offset().top -
        60
      );
  }

});