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You should have folders named for the app with a .3dsx and a .smdh named the same as the folder. Any files in the 3ds folder should be .3dsx (will be an app without an icon). Any other files would be useless.The 3ds folder, should there be any loose files in it or just folders? I seem to have numerous files in the 3ds folder. If these files are not suppose to be there, could this cause duplicate apps showing up on homebrew?
Thanks,
ISO-Man