How to organize a larger PHP project

I'm trying to organize a larger PHP project with more than 50 files in code, not counting the resource files.

It looks like this:

administrator files (php code and resource files)
database framework
resource files (images, templates, including PHP templates, CSS)
CSS files
scripts (Javascript and jQuery)
PHP code (classes, controls)
PHP and HTML scripts (acting as pages, placed in root)

How does one, properly organize a larger PHP project like this one?

Solution

First of all, a project that holds 50 files is not even called a project, in the real concept of the word.

Take a look at how the most used frameworks do that and you will get a place to start.

Some PHP frameworks:

So you can have a good reference, there is a simple good practice on PHP projects that tells that only the template, stylesheet and scripts files should be in a public directory, such as /var/www on your host. All the core application should be on a higher-level structure, for example:

src/ (The core application)
public/ (The public directory)
    css/
    img/
    js/
    index.php

You can, then, have a .htaccess file on the public directory as well, so you can control the requests.

But again, project architecture and structure organization goes a lot further than those simple tips.