I have been looking a lot online and I have always thought that Google's spiders saw the code, but after research it seems as if this isn't true. I am knew to seo and haven't had much experience yet. I especially wanted to know if Google could see include files in PHP and it seems that this is true. I just haven't been able to find an answer to whether Google actually sees my code. Any help would be great.
PHP is a Server Side Scripting Language which is responsible for rendering an HTML output.
A bot acts exactly like a browser client, and will only see the rendered HTML output of any scripts.
No, your PHP code is never seen by a bot, or any client.