The downloadable distribution of CodeIgniter and many other PHP frameworks have those file and boilerplate to protect badly configured Apache setups where the u

The downloadable distribution of CodeIgniter and many other PHP frameworks have those file and boilerplate to protect badly configured Apache setups where the user just unzips the downloaded distribution into public_html. If you have .php files handled by PHP, or you have the mod rewrite htaccess rules enabled, the PHP files won't be exposed to the user. None of these are necessary if you have properly configured your web server.