If element is in view, get href from link then substrat href before hash to find the link to add active class + Scroll to anchor

navigation.js

function scrollToAnchor(aid){
  var aTag = $("a[name='"+ aid +"']");
  $('html,body').animate({scrollTop: aTag.parents().offset().top - 100},'slow');
}

var sections = $('.content-section')
, nav = $('.page-navigation')
, navLink = nav.find('a').attr('href')
, navHash = navLink.substr(0,navLink.indexOf('#'))
, nav_height = nav.outerHeight();

$(window).on('scroll', function () {
  var cur_pos = $(this).scrollTop();
  sections.each(function() {
  var top = $(this).offset().top - nav_height,
  bottom = top + $(this).outerHeight();

  if (cur_pos >= top && cur_pos <= bottom) {
    nav.find('a').removeClass('active');
    sections.removeClass('active');
    $(this).addClass('active');
      var marker = $(this).children('.marker').attr('name');
      nav.find('a[href="'+ navHash +'#'+ marker +'"]').addClass('active');
    }
  });
});

$('.page-navigation li a').on('click', function (e) {
  $('.page-navigation li a').removeClass('active');
  $(this).toggleClass('active');
  var link = $(this).attr('href');
  var hash = link.substring(link.indexOf('#')+1);
  scrollToAnchor(hash);
});