Ebook: Developing Large Web Applications: Producing Code That Can Grow and Thrive

The book essentially covers how to code up a large application without a framework. In reality if you are working with a large application (or not) you should use an existing framework to manage PHP, HTML templates, and JavaScript. For example CodeIgniter, (I haven't found a PHP HTML templating system I like yet), and Dojo.

tl;dr - has some stuff you should know, but better to let a framework(s) do it for you.