Yes it does matter where you obtain your copy of FTMM3. The MAS version stores files in the user's library due to MAS sandboxing. See
https://developer.apple.com/app-sandboxing/ As an example, the Apple iBooks app in Mavericks & Yosemite stores book files in ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books
Go and try out newer versions of Mac OS. 10.8 did away with the dock alias to the user's documents folder. If you do not understand what we mean by MAS, see
http://www.apple.com/osx/apps/app-store/ &
https://itunes.apple.com/us/app/id871254880?mt=12No-one here has moved or deleted any files and it is getting rather irritating having you continually insinuate that the users are the problem. Once again I have flagged your posts.