When I start a new project with CodeIgniter (CI) i start to organize everything.
The original setup is something like this:
I don't like that at all.
This is my way!
If your base-folder is htdocs, it's no longer possible for the users to have access to your application and systems folder.
And the renaming is so that I can easily switch between two versions back and forth (and keep track of what version I'm currently using).
The paths to your application and system-folder are changed in index.php