Structure of project and readme

Create a proper readme for anyone interested to be able to understand the project and its flow.

Structure the files properly. There are so many files in root which looks cluttered. Put utilities and classes in directories, leaving only important and config in root.

Document well the files with few comments.

Start by inventorying the repository root, then identify the utilities and classes that should be grouped into directories. Read the existing project files and trace the project flow before defining the structure. Done means a clear README, an organized root, and useful comments throughout the files.

Written by the indexing model from the issue text.