I've seen that this has been requested many times over a long time.
To help the dev's, I thought maybe we can put all of our thoughts together to get all the features clear
Here is my mock up of the option tab, lets make it perfect. I can photoshop all ideas to update it.
In my mock up:
1. You can leave the tick box un-ticked and the default portable apps tree structure stays or tick the box and design the structure yourself.
But this may have issues if someone ticks the box, changes many things then un-ticks the box (thoughts) maybe just no tickbox?
2. You can change the order of the folders by highlighting a folder and press the "move up" button
3. You can remove a folder (to be safe it should leave the physical folder there for you to manually delete it yourself, so that if a mistake is made data is not lost).
4. You can add a new folder, set its path, pick the menu folder icon and windows icon. (folder needs to be manually created before you do this which is shown by you have to use the select button (search for the folder))