Does Directory Structure Effect SEO ?

[eluser]Unknown[/eluser]
Hello, I'm currently auditing Codeigniter for an upcoming project.

I'd like to keep the maximum amount of code out of public directories. Ideally I'd like only a single index.php file in the public www directory making calls to restricted code in a folder higher in the structure, the root folder (for example).

My question is "how will this affect search engine optimization?"

I suspect that having the "view" files out of public view will hinder web crawlers.

I'm wondering if I will want to cache pages in a public folder so that the crawlers will be able to index the site effectively.

I'd appreciate any feedback.

Thanks.