The folder names you can and can't use seem to be defined in the 'VirtualFolders.cfg' file in the Core Library, mine is here :
C:\ProgramData\Ableton\Live 9 Standard\Resources\Core Library\Ableton Folder Info\VirtualFolders.cfg
You'll see each 'virtual folder' has a pattern associated with it which defines the names it'll detect from the user library and packs I presume.
Not played with it much yet, but have been able to add my own top level folder to the Sounds category.
In the xml file I added this :
<VirtualFolder Name="MDK" Patterns="MDK"/>
within the Sounds virtual folder group, then I created a directory :
C:\ProgramData\Ableton\Live 9 Standard\Resources\Core Library\Sounds\MDK
Now if I add MDK folders within the User Library (e.g. Presets -> Instruments -> Operator -> MDK) and add content then it shows up in my MDK folder in Sounds. It doesn't show up in the Instruments -> Operator section though. Not worked out how to sort that out or if its possible.
At least it's a start.
Before Live 9 the first thing I did was to delete pretty much all the factory content (presets, clips, samples etc..) because I never use them, hopefully I'll find a way to clear all the crap out of this version as well otherwise most of the browser is just clutter. I dont like clutter.
I did this on a mac. I added a virtual folder
<Folders> <VirtualFolder Name="Fran" Patterns="Fran"/>
/Applications/Ableton Live 9 Beta.app/Contents/App-Resources/Core Library/Ableton Folder Info/VirtualFolders.cfg
and added an actual folder
/Applications/Ableton Live 9 Beta.app/Contents/App-Resources/Core Library/Sounds/Fran
It shows up in Sounds as a category with a Rack I simply dragged from a set into a folder I made directly inside Live (right click, select 'new folder') called Fran in the User Library