system: Most importantly, this directory contains the core files which are required for Codeigniter, for example here every setting is used to bootstrap the CI application like Database connection is made, hooks are activated and every libraries which Codeigniter is dependent on gets initialized. As a newbie developer one is not advised to touch any file or setting here, as it is considered as operating system of codeigniter.
application: This folder is the one we’ll be spending most of our time in. It’s where all of the code specific to our app will live, including all of its models, controllers, and views.
index.php: Every http request coming from user is first captured at index.php. Here CI checks each setting of application i.e bootstrapped, application environment is checked and according to it error reporting is done and if everything is good then it gets routed to a default route or base route.