The directory structure of the framework is logically separated based on their purpose. It is simple and easily understandable. However, if you wish you may customize it, but make sure you are changing PSR-4 settings available in composer.json You can find index.php in the root directory which is the entry point of your application.
This directory contains the files which boots your application. Do not change any code unless you are aware what you are doing.
This directory is the entry point of your console application. Craft is the name of your console application available in cygnite.
This is where your actual application code resides. All your application configuration, classes, model, views and logic goes here. Application directory structure looks like below.
By default cygnite also provides you to use HMVC structure. If you wish to build a widget application with modular design you may use modules. Modules directory structure looks like below:
This directory contains all your packages required for your application. You can install any third party packages here, composer will autoload classes.