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 ?!