使用单个codeigniter基本文件夹运行多个应用程序

I found the official document quite confusing for folder structure about creating multiple application on single base folder of CI (CodeIgniter).

Here: Managing your Applications

Let say i have a base folder /ci under web root directory /www so my project folder structure is

/www/ci

Now according to the mentioned tutorial in above link, if i create myapp1 sub-folder under /application folder of ci will be

/ci/application/myapp1

main index.php path: /ci/index.php

myapp1/ folder structure: (below)

In official tutorial link, they have mentioned /applications instead /application to confuse us more

/config

/controllers

/libraries

/models

/views

Now if i update $application_folder the main index.php file /ci/index.php to point to this application folder will be

$application_folder = 'application/myapp1';

I can access it using route

http://localhost/ci/

Question:1 But it will no longer be able to use the main application folder /ci/application or if i create new application myapp2 sub-folder inside application folder, then how to access it?

Question:2 According to documentation:

Each of your applications will need its own index.php file which calls the desired application. The index.php file can be named anything you want.

But the million$ question is where to put those own index.php files?

Note: I am not asking about the 2nd method of having separate new application folders parallel with main application folder. I have already successfully implemented it.

Use following structure:
/www/ci1 directory for 1st site
/www/ci2 directory for 2nd site

Both ci1 and ci2 will be same structure and will contain index.php file. under ci1 and ci2 structure will be as follow:

/config
/controllers
/libraries
/models
/views
index.php

and system the directory is /www/system.

Now change:

$system_path = 'system' to $system_path = '../system' in both index.php

And you are done. You can access both site ci1 and ci2. if you want ci3,ci4, ... cin you can just create a new folder and change in index.php