Hmmm. My fix for this issue reveals that this is also happening with a handful of games extras, where the same file is part of both goodies and special edition upgrades. The issue is less serious there however as extras generally don't have MD5s and the size for both is exactly the same. I should probably check for that to avoid downloading unnecessary duplicates.
Kalanyr: As far as I can tell they are supposed to be identical, both versions are installers but as they have different sizes / md5s there must be something different about it. The size difference seems to small for it to be Galaxy bundling, it might be one is installing a slightly out dated version of the game ?
timppu: I might be daft but I still don't get it. Why are there two separate links in the game's download page for files which are supposed to be identical (but in reality are not)? Can you give a screenshot of such download page?
Sure.
Hard West has been fixed at some stage, it no longer has duplicates.
Examples of the Bad Stuff:
Reigns
(fixed) GOGRepo Output
[setup_reigns_64_1.25_gog-3_(10889).exe] -- Reigns (Part 1 of 2)
version: 1.25 gog-3
[setup_reigns_32_1.25_gog-3_(10889).exe] -- Reigns (Part 2 of 2)
version: 1.25 gog-3
[setup_reigns_32_1.25_gog-3_(10889)(1).exe] -- Reigns 32-bit version
[gog_reigns_2.1.0.3.sh] -- Reigns
version: 1.25
(Which means that Part 2 of 2 and the 32 bit version in the Screenshot have the same filename, you can see in the screenshot they have different sizes, they also have different MD5S (which you'd hope is the case since a matching MD5 on different file sizes is always a false positive by collision in any case).
Walking Dead Michonne
(fixed) GOGRepo Output
game items.....:
[setup_the_walking_dead_-_michonne_episode_3_(2699).exe] -- The Walking Dead: Michonne - A Telltale Miniseries (Part 1 of 6)
version: Episode 3
[setup_the_walking_dead_-_michonne_episode_3_(2699)-1.bin] -- The Walking Dead: Michonne - A Telltale Miniseries (Part 2 of 6)
version: Episode 3
[setup_the_walking_dead_-_michonne_episode_3_(2699)-2.bin] -- The Walking Dead: Michonne - A Telltale Miniseries (Part 3 of 6)
version: Episode 3
[setup_the_walking_dead_-_michonne_episode_3_(2699)(1).exe] -- The Walking Dead: Michonne - A Telltale Miniseries (Part 4 of 6)
version: Episode 3
[setup_the_walking_dead_-_michonne_episode_3_(2699)-1(1).bin] -- The Walking Dead: Michonne - A Telltale Miniseries (Part 5 of 6)
version: Episode 3
[setup_the_walking_dead_-_michonne_episode_3_(2699)-2(1).bin] -- The Walking Dead: Michonne - A Telltale Miniseries (Part 6 of 6)
version: Episode 3
[patch_the_walking_dead_michonne_2.1.0.4.exe] -- Patch gog-4 (episode 2)
version: (gog-3) -> (gog-4)
[patch_the_walking_dead_michonne_2.2.0.5.exe] -- Patch gog-5 (episode 3)
version: (gog-4) -> (gog-5)
Parts 1-3 and 4-6 have the same file names. In the screenshot it looks like they have the same size , but that's due to rounding, they have different file sizes when expressed in bytes (or even Kilobytes in some cases) , and they of course have different MD5S.
The weird stuff
Shadowgate
This has the same files listed in extras and special edition, but they are zips and have precisely matching sizes and no MD5 and the internal CRC of both is valid so this never caused issues before, I won't bother with a screenshot the matches are exactly what you'd expect where the same name occurs in Goodies and Special Editiion.
(The same thing happens with Gods Will Be Watching, Lords of Xultima, Wasteland 2 (but not the Director's Cut edition where lower version goodies were properly accounted for),
I should probably tinker with my fix and let these through if they have exactly matching file sizes and MD5s , to cut down on wasted space / downloads.