Indeed, I've tested it myself. The reorganisation doesn't have any effect, but then it only shows you the flat menu asnyway - so I don't think it makes any sense in the world of Catorise. System for "User Guide" seems appropriate and it went there because it's a nicely behaved built-in package which contains a freedesktop.org Categories line in its .desktop file :-)

Plug: v0.8.0 of Catorise hit Extras today.