No longer able to group applications into folders in the Applications folder?

I would like to group applications in Folders in the Applications Folder, which I have dragged back to to the dock.  This is the way I had managed apps in Snow Leopard.  I can create folders no problem,but when I try to drag apps into these folders, a copy is always left behind in the Applications folder.  How do I move the app?   I am not able to delete the copies that are left behind.
My Account has Admin rights, and this is a clean install into an empty partition....I wanted to check out Lion before moving from SL.
Launchpad is pretty, but I prefer the Applications Folder.

It does cause problems in a number of circumstances.
In this forum alone, there are several threads with many users who used Setup Assistant or Migration Assistant to transfer their stuff, ended up with lots of duplicate apps because of it, and had great difficulty finding and deleting the duplicates.
There have also been folks whose apps did't get updated, and Adobe apps that wouldn't run at all.
Again, it depends on the apps and circumstances.

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