Design Logic Help Requested

...
Some people get in this mode where they think the application folder has to be named  'application', and the system folder has to be named 'system'. This is even implied in the docs for upgrading. The main index.php file is where the file path for the application and system folders are. So you can go in that file, and change those settings. Then you can name your system folder something relevant like "system306" and your application folder "alphajuly2016" .

Then by creating a folder - with the main index.php file inside of it - that version of the application is directly available. So like a folder called 'alpha' - you set which system and application folder its using - then example.com/alpha will pull up that version. example.com/beta can pull up the beta version. and you can link between the two of them.

So then for example - if you have a bunch of public website functionality. And an admin area with completely different functionality. There is no reason they need to be sharing the same application folder - and there are many reasons why they should not be. Similar if you are building something - when you have something stable you can split it off. And then when you are working in your alpha folder and you do something to a route file that kills the application - you have not affected your beta version because its in a completely separate application folder.
...

Hey, can you help clarify this for me? I want to get this "alpha" "beta" structure set up from the get go so I know how it all works down the line. I'm basically going about it exactly as you've mentioned above, but I'm missing something when it comes to making the "alpha" folder with the main index.php inside of it. Is the only thing inside the "alpha" folder the index file....or is the 'alphajuly' application directory in there as well? If I'm moving the main index file...doesn't something else have to point to where that is? is there also a "beta" folder with an index.php file pointing to the "betawhatever" application directory? And is there a reason that I would need multiple systems folders? ie: one for the beta version and another for the alpha version, or am I looking at that all wrong? Oh, and I'm thinking I probably need to have a .htaccess file that matches each of these as well?

Sorry if I sound like a lost puppy on this!

In the documentation (that I obviously missed my first time around...) it states that in order to support a multiple application structure...to basically just nest everything that is inside the application folder inside a subfolder (and then point to one or the other in the main index.php...I can see how that might work too, but I'm curious about your structure and would love to gain some more comprehension when you have a moment!

Thanks so much!