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index.php is the (single) entry point of your application. You don't need to create new entry files for every page (products.php, guestbook.php, etc.) - this is where controller classes come into play.
framework directory is a copy of the Integry Framework. The directory can have a different name, just make sure to adjust it in the index.php file.
application directory is where your application code resides in. It usually has 2 or 3 (or more) subdirectories.
As the bare minimum, IF expects it to have at least the controller subdirectory, so that there would be anything to execute. The controller classes reside in this directory.
Usually the controller actions refer to renderable page templates, so in most cases there's also a view subdirectory, that includes them.