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Menu transition

I'm trying to rebuild not copy and paste this website http://paramoredigital.com/ only for learning direction. I have problem with menu transition, more precisely If you click top-right button menu will show up smoothly and I don't know how to do it in my code.
Here is my code https://github.com/Szuchow/paramore-digital.

Click on the X and the menu will appear. The rest is a matter of styling.
$("body").on("click", function() {
$(".menu").addClass("open");
})
body {
padding: 0;
}
.container {
width: 100vw;
height: 100vh;
background: lightblue;
}
.menu {
position: absolute;
top: 0;
left: 0;
opacity: 0;
background: pink;
transition: opacity 1s ease;
width: 100vw;
height: 100vh;
}
.menu.open {
opacity: 1;
}
.toggle a {
font-size: 2em;
text-decoration: none;
cursor: pointer;
}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<div class="container">
<span class="toggle">X</span>
<div class="menu">
<ul>
<li>Option 1</li>
<li>Option 2</li>
<li>Option 3</li>
</ul>
</div>
</div>

Nested z-index layering with unexpected results

Fiddle.
Description of problem:
When clicking the Click me button, the .list element fades in on top of the Menu button, in spite of it having a lower z-index value. I assume it has to do with inheritance, but I have explicitly specified a higher z-index value for the .keep-on-top element, so I'm confused by the behavior I'm seeing.
Desired outcome:
I would like for the .list element (i.e. the black box) to fade in beneath the menu button but above the blue .header-color div. I welcome any solutions.
Code:
HTML:
<div class="header">
<div class="header-color"></div>
<div class="keep-on-top"><button>Menu</button></div>
</div>
<div class="list">
<ul>
<li>Item 1</li>
<li>Item 2</li>
<li>Item 3</li>
</ul>
</div>
<br/><br/><br/><br/><br/><br/>
<button>Click me!</button>
CSS:
.header {
position: absolute;
top: 0;
left: 0;
width: 100%;
height: 100px;
z-index: 2;
}
.header-color {
background-color: #0099cc;
position: absolute;
top: 0;
left: 0;
width: 100%;
height: 100px;
z-index: 1;
}
.keep-on-top {
position: absolute;
color: #fff;
z-index: 4;
}
.list {
background-color: #000000;
position: absolute;
z-index: 3;
color: #fff;
display: none;
}

Remove z-index from class header

Anchor scrolling with pure js?

So all the solutions that I can find use jQuery. I understand it might be easier to use jQuery, but does anyone know of a pure Javascript method of anchor scrolling?
Codepen to get started: http://codepen.io/mildrenben/full/Kwwdzb/[1][1]
HTML:
<nav>
<ul>
<li>Section One</li>
<li>Section Two</li>
<li>Section Three</li>
<li>Section Four</li>
<li>Section Five</li>
</ul>
</nav>
<main>
<h1 id="section-one">SECTION ONE</h1>
<h1 id="section-two">SECTION TWO</h1>
<h1 id="section-three">SECTION THREE</h1>
<h1 id="section-four">SECTION FOUR</h1>
<h1 id="section-five">SECTION FIVE</h1>
</main>
CSS:
html, body {
width: 100%;
height: 100%;
}
* {
margin: 0;
font-family: sans-serif;
}
h1 {
margin-bottom: 300px;
}
nav {
width: calc(20% - 60px);
height: calc(100% - 60px);
background: aquamarine;
float: left;
padding: 30px;
overflow-y: scroll;
}
nav ul {
list-style: none;
}
nav li {
margin: 30px 0;
}
main {
width: calc(80% - 60px);
height: calc(100% - 60px);
background: darkseagreen;
float: left;
overflow-y: scroll;
padding: 30px;
}
main p {
width: 35%;
margin: 10px 0 70px;
}

Messy mouse events in chrome

In IE or Firefox the site works like this (IE11):
(Tabs are clickable)
but not in chrome. Click on tabs not get fired. I tried to reveal element in Developer Tools, but it reveals #container element instead of the lielement I clicked on.
It looks like the layering of the elements are not the same as you see it and when you raise an event (ex.: click). The first/parent div is the top element and the tabs (li) are nested behind.
Why is it working in IE and Firefox, and why does not in Chrome? What is the differecnce?
$('button').click(function() {
$('.box').toggleClass('flipped');
})
$('li').click(function() {
var text = 'You selected ' + $(this).html();
alert(text);
});
* {
margin: 0;
padding: 0
}
button {
position: fixed;
right: 5px;
bottom: 5px;
}
.box {
position: relative;
width: 300px;
height: 300px;
transform-origin: right center;
transition-timing-function: cubic-bezier(1.000, 0.000, 0.000, 1.000);
transition: all 300ms, transform 500ms ease;
}
.box figure {
position: absolute;
width: 100%;
height: 100%;
transition: visibility 0s ease 140ms;
}
.box:not(.flipped) figure.back {
visibility: hidden;
}
.box.flipped {
transform: translateX(-100%) rotateY(-180deg);
}
.box .front {
background-color: skyblue;
}
.box .back {
transform: rotateY(180deg);
background-color: lightgreen;
}
.box .back .nav {
position: absolute;
top: 0;
left: 0;
right: 0;
height: 32px;
width: 100%;
background-color: skyblue;
text-align: center;
}
.box .back .nav li {
background-color: white;
width: 24%;
display: inline-block;
height: 30px;
line-height: 30px;
}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<div>
<div class='box'>
<figure class='front'>
<p>FRONT SIDE</p>
</figure>
<figure class='back'>
<ul class='nav'>
<li>Menu 1</li>
<li>Menu 2</li>
<li>Menu 3</li>
<li>Menu 4</li>
</ul>
<div class='content'>
<p>BACK SIDE</p>
</div>
</figure>
</div>
</div>
<button>FLIP</button>
Thanks in advance for any help!

To be 100% saint with your work, wrap your JS code in
$(document).ready(function(){ ... })
Secondly I would not advise to use such big qualifiers $('li'). This will scan every list element in DOM tree-slow and not advised. Here you are interested in list elements from menu only.
I would also find Flip button by id, you have only one button, so it doesn't cost much:)
I would propose something like this :
var navContainer = $('.box > figure.back > ul.nav');
navContainer.on('click', 'li', function(){ ... })
This code should work, even when you add more li items to DOM.
Secondly you could in debug mode find, if this navContainer has been found or not.

I found a workaround for my problem. If I set z-index: 0 and position: relative to body and the body > div then clicks get fired.
SOLUTION : CSS
body, body > div { position: relative; z-index: 0; }
$('button, .front').click(function() {
$('.box').toggleClass('flipped');
})
$('li').click(function() {
var text = 'You selected ' + $(this).html();
alert(text);
});
/*Workaround*/
body,
body > div {
position: relative;
z-index: 0;
}
/************/
* {
margin: 0;
padding: 0
}
button {
position: fixed;
right: 5px;
bottom: 5px;
}
.box {
position: relative;
width: 300px;
height: 300px;
transform-origin: right center;
transition-timing-function: cubic-bezier(1.000, 0.000, 0.000, 1.000);
transition: all 300ms, transform 500ms ease;
}
.box figure {
position: absolute;
width: 100%;
height: 100%;
transition: visibility 0s ease 140ms;
}
.box:not(.flipped) figure.back {
visibility: hidden;
}
.box.flipped {
transform: translateX(-100%) rotateY(-180deg);
}
.box .front {
background-color: skyblue;
}
.box .back {
transform: rotateY(180deg);
background-color: lightgreen;
}
.box .back .nav {
position: absolute;
top: 0;
left: 0;
right: 0;
height: 32px;
width: 100%;
background-color: skyblue;
text-align: center;
}
.box .back .nav li {
background-color: white;
width: 24%;
display: inline-block;
height: 30px;
line-height: 30px;
}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<div class='container'>
<div class='box'>
<figure class='front'>
<p>FRONT SIDE</p>
</figure>
<figure class='back'>
<ul class='nav'>
<li>Menu 1</li>
<li>Menu 2</li>
<li>Menu 3</li>
<li>Menu 4</li>
</ul>
<div class='content'>
<p>BACK SIDE</p>
</div>
</figure>
</div>
</div>
<button>FLIP</button>

jQuery - DIV to move with scrolling motion and stick position to top and bottom of window

There may be already a jQuery plugin which can achieve this, but I can't find one to do exactly what I'm after. If there is, just point me to the tutorial, thanks.
My problem I have is that I have very long page content, and my sidebar is not visible when you are scrolled near the bottom of the page.
So I would like to make my #sidebar div to stick to the top and bottom of my browser window as you scroll up and down the page.
My sidebar height is longer than your typical screen resolution, so I need the bottom of sidebar to sticky to the bottom of the browser window as well as the top of the browser.
So as you begin to scroll down, the side bar will scroll like normal, but when you reach the end the sidebar, it sticks and will not scroll, and as you begin to scroll up, the sidebar will follow until the top of sidebar reaches the browser, then it sticks. Vice Versa.
Is this possible?
I have created a jsfiddle of simple design layout which is central. I have added a dotted border to the sidebar so you now where the sidebar should stick.
http://jsfiddle.net/motocomdigital/7ey9g/5/
Any advice, or you know a online tutorial or demo, would most awesome!
UPDATE
Please see this attempt by #Darek Rossman
http://jsfiddle.net/dKDJz/4/
He's got the basic idea working. But the scrolling up, causes it to snap to the top. I need the sidebar to be fluid with the scrolling up/down motion. But sticking to the either the top or bottom of the window. It should also not be fixed positioned when the header/footer are in viewport, so it does not overlay.
Thanks

I have updated the jsfiddle with my solution.
var $sidebar = $("#sidebar"),
$window = $(window),
sidebartop = $("#sidebar").position().top;
$window.scroll(function() {
if ($window.height() > $sidebar.height()) {
$sidebar.removeClass('fixedBtm');
if($sidebar.offset().top <= $window.scrollTop() && sidebartop <= $window.scrollTop()) {
$sidebar.addClass('fixedTop');
} else {
$sidebar.removeClass('fixedTop');
}
} else {
$sidebar.removeClass('fixedTop');
if ($window.height() + $window.scrollTop() > $sidebar.offset().top + $sidebar.height()+20) {
$sidebar.addClass('fixedBtm');
}
if ($sidebar.offset().top < 0) {
$sidebar.removeClass('fixedBtm');
}
}
});
h1, h2 {
display: block;
font-weight: bold;
}
#horizon {
width: 100%;
height: 100%;
min-height: 100%;
background: #cccccc;
overflow: hidden;
}
#header, #footer {
width: 480px;
height: auto;
overflow: hidden;
background: teal;
padding: 10px;
color: #ffffff;
}
#wrapper {
width: 500px;
height: auto;
overflow: hidden;
background: #ffffff;
margin: 0 auto;
}
#content-wrapper {
width: 100%;
height: auto;
overflow: hidden:
}
#content {
width: 330px;
height: auto;
overflow: hidden;
background: #ffffff;
margin: 0 auto;
float: left;
padding: 10px;
}
#sidebar {
width: 130px;
height: auto;
overflow: hidden;
background: #ffffff;
margin: 0 auto;
float: left;
clear: right;
padding: 8px;
background: #e5e5e5;
border: 2px dashed red;
}
.fixedBtm {
margin-left: 350px !important;
position: fixed;
bottom: 0;
}
.fixedTop {
margin-left: 350px !important;
position: fixed;
top: 0;
}
.post {
margin: 5px;
width: 320px;
background: red;
float: none;
overflow: hidden;
min-height: 175px
}
.buttons li {
margin: 5px;
width: 120px;
background: blue;
float: none;
overflow: hidden;
min-height: 20px;
text-align: center;
color: #ffffff;
cursor: pointer;
}
.buttons li:hover {
background: lightblue;
}
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<div id="horizon">
<div id="wrapper">
<div id="header">header</div>
<div id="content-wrapper">
<div id="content">
<h1>Latest Posts</h1>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
<div class="post">This is a post</div>
</div>
<div id="sidebar">
<h2>Sidebar</h2>
<ul class="buttons">
<li>Button 1</li>
<li>Button 2</li>
<li>Button 3</li>
<li>Button 4</li>
<li>Button 5</li>
<li>Button 6</li>
<li>Button 7</li>
<li>Button 8</li>
<li>Button 9</li>
<li>Button 10</li>
<li>Button 11</li>
<li>Button 12</li>
<li>Button 13</li>
<li>Button 14</li>
<li>Button 15</li>
<li>Button 16</li>
<li>Button 17</li>
<li>Button 18</li>
</ul>
</div>
</div>
<div id="footer">footer</div>
</div>
</div>
The sidebar should remain in place at the top when the window is larger than the sidebar and fix to the bottom when the sidebar is larger.

You don't need any jQuery or javascript for this. All of this can be achieved in CSS with position: fixed.
Change your sidebar selector to the following
#sidebar {
width: 130px;
height: auto;
overflow: hidden;
background: #ffffff;
margin: 0 auto;
clear: right;
padding: 8px;
background: #e5e5e5;
border: 2px dashed red;
position: fixed;
right: 35px;
}