Anywayz, here’s how it should look:

project_dir/
- php/
- – config/
- – - config.php
- – init.php
- – lib/
- – - mysql.php
- – - lib.php
- – main.php
- – templates/
- – - _footer.php
- – - index.php
- – - page1.php
- – - _header.php
- web/
- – css/
- – - base.js
- – index.php
- – js/
- – - basejs.js
- – images/
- – - whatever.png

project_dir/
php/
config/
config.php
init.php
lib/
mysql.php
lib.php
main.php
templates/
_footer.php
index.php
page1.php
_header.php
web/
css/
base.js
index.php
js/
basejs.js
images/
whatever.png

You should place your project folder outside you web server’s public or www dir (or whatever it’s called) and tell the web server that it can read from your project’s web dir (e.g. with a symbolic link or a virtual host). The index.php in your web folder should include or require your main php file.

Also, you should use HTML templates in PHP to try and separate your PHP and HTML as much as possible. This requires you to write or use a template engine so it’s more work in the beginning but you’ll greatly profit later on because your code doesn’t get all messy.

And when you’re working on a big PHP5 project and learning something new doesn’t scare you, you should try Symfony, it’s a PHP framework that helps you build projects. It takes a while to learn but once you do it’s great.

http://www.symfony-project.org/

I hope this helps
Greetings,
Thomas

When PHP is in the game, how do you deal with all those files?