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Doomsday\data\Doom\Addons\SFX_(deus-ex_edition).pk3
Doomsday\data\Doom\Addons\SFX_Secret_(deus-ex_edition).pk3
Doomsday\data\Heretic\Addons\SFX_(deus-ex_edition).pk3
Doomsday\data\Heretic\Addons\SFX_Secret_(deus-ex_edition).pk3
Doomsday\data\Doom\Addons\jDoom_SFX_(deus-ex_edition).pk3
Doomsday\data\Doom\Addons\jDoom_SFX_Secret_(deus-ex_edition).pk3
Doomsday\data\Heretic\Addons\SFX_(deus-ex_edition).pk3
Doomsday\data\Heretic\Addons\SFX_Secret_(deus-ex_edition).pk3
Comments
The reasoning being, the parent folder(s) cannot be considered a part of the ID because they may change and almost certainly will be different depending on the computer the file is being used.
If the PK3 contains metadata in an Info file, the version could be defined there manually. (The Info is also used to determine the default tags for the mod.)
In the first case, I think it should have shown the two different versions of the file, though... I'll give this a test.
So the best approach would be to have unique file names.