I only keep a copy of the SH3 folder in (My) Documents and the total MODS folder (for JSGME) in the game's base folder if I need to reinstall. Before I use JSGME again after reinstal is finnished I first delete the hidden folders and jsgme.ini file (in MODS) left over from the old JSGME. Oh yeah, don't forget the Personell Files folder made by SH3 Commander if you use it. Everything else is recreated by game install or patch and (super)mods.
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