IMHO, the project map is simply an inventory of working windows and would not be folderized. They have no intrinsic view settings and so are just an index of the workspaces you've created. Try devising a scheme to index them via their Reference IDs. Sections Elevations, detail and worksheets will sort via their RefID.
We need folder Structures to be sure but GS would be better serving us by incorporating them in places like the Complex Profile Manager and the Layer Manager.
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