Organize php project files

Question

I'm new to the web development, recently I create a web application with Php/Mysql, and now I want to put it on to the server but I feel that my files organization is bad (very bad).

my project files structure looks something like that

|--XAMPP htdocs
    |--MyProject
        |--config.php
        |--functions.php
        |--header.php
        |--nav.php
        |--index.php
        |--js   
        |--css
        |--images
        |--register
            |--index.php
        |--messages
            |--inbox
                |--index.php
                |--handle_inbox.php
            |--outbox
                |--index.php
                |--handle_outbox.php
            |--trash
                |--index.php
                |--handle_trash.php
            |--uploaded_files
        |-- ...

what I can do to improve this structure and make it secure ?!

Answer 1

Paul M. Jones has done some fantastic research into common practice of tens of thousands of github projects in the realm of PHP. He has compiled a standard filesystem structure based on this research. Take a look at the Standard PHP Package Skeleton and base your project off of it.

You do not need all of the file structure that he recommends, but it's a great place to start. If you are planning to open-source your project, this file structure will make the most sense to your potential contributors and users.