Im creating a website and i am very OCD when it comes to security so i heard that if you store all of your .php files outside of your public_html folder and invoke them with another .php file that is inside your public_html folder then your risk of an attack is lower. Is this true, if so how would i do this. I read something about using .htaccess but I'm not sure if that was the correct way to do it. I though i could maybe use include but im not sure how include works with parameters.
How to invoke a php file that is located outside public_html
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See PHP include function: http://www.php.net/manual/en/function.include.php
However, I doubt what you're trying to do will increase security. Where did you hear that it increases security?
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There isn't a huge amount of extra protection offered by this strategy. Mainly, it ensures that if your server is misconfigured and fails to send PHP scripts to the PHP interpreter, it doesn't allow PHP code to be sent directly down to the browser.
You don't store all your PHP scripts outside document root. You typically store only files which are not intended to be accessed publicly outisde the doc root. Store your include files outside the doc root and include them as you would any file. Store files which are are public views inside the document root, as they need to be web-accessible.
There is a design pattern known as the Front Controller pattern whereby a single index page (index.php) accepts routes and includes other files as appropriate. Numerous PHP frameworks support this out of the box.