What are the steps to start developing a web application (php+ mysql) in a professional way? Documented steps in professional companies?

You can design the document as you like:

Contents:

1. What is it

2. Architecture

3. Module types

4. Tools

5. Engine

6. Database

7. Administration

8. Platform

9. Extendibility

10. Team / Responsibility 

Most of the explanations it goes inside the working files like a comments: /**

 * Why I'm doing this and what will be the result

 **/

What About USE CASE and STORYBOARD specialy in a website development in real world as a documented process

First 

1. Design an architecture

   Look what you really have to do

   How many sections you have to create.

   Which Programming tools you will need (eg Dreamweaver, Xampp, My sql)

   Which type of code you are going to use to make this happen?

   Will you need any bundled app? (E.g. Jquerries, ajax, )

   If E- Commerce which cart will you use open cart?3d cart? joomla??

first of all we should recognize the time required for the development so that we can choose a best process model to assure the quality of product. The first phase should be requirement gathering/understanding and then identifing all use cases.