Shiwund, yes you're correct.
My "ManagedContent" and "UserData" subfolders are now empty; left overs from some old file shuffling.
If you're wondering, FileSystem.CFG dictates my preferred folder organization and reads as follows:
Data=$[AssemblyFolder]\Data\
Settings=$[AssemblyFolder]\Settings\
RestartProcess=$[AssemblyFile]
RestartArguments=/FileSystem=FileSystem.CFG
ManagedContent=$[AssemblyFolder]\ManagedContent\
InitialRoute=$[AssemblyFolder]\..\RailWay\
InitialTrain=$[AssemblyFolder]\..\Train\