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I was checking the RMG this evening. I figure there is still things occurring.

The Shadow gate spawning inside mountains and in the water is probably because they are set as caves. Looking in the level generator.Rpk makes me think the game consider shadow gates as water caves respectively cave entrances placed in mountains. There might be no way around it.

But in case I start to fiddle with it. I will create a separate RMG clone and experiment little what goes where. It's a small priority at the moment. I have two screens to play around with so I can compare mod editor "A" with mod editor "B" at the same time.

In general I will also experiment with package manager to make an steam update if possible. I'm not sure it will create a duplicate or update the mod in the steam workshop. If it does I will just remove it from steam workshop.
 
I tried to update the mod through the launcher today on steam workshop.

The only thing that happens is that I uploaded a second mod. That means its only Dr K who can update it.