If I recall correctly, one of the main reasons for replacing the clouds was a technical one: Previously, the clouds were giant mesh particles drawn in the 3D. This meant the camera's far clip plane needed to extend far enough to cover all of the clouds, otherwise they would get cut off on the left and right edges of your screen. Regardless of graphics settings the far clip plane was something like 4 kilometers. I wanted to make it configurable so that players on low-spec PCs could cull more distance objects (think of how area increases as circle radius increases). By moving all of the sky effects like sun, moon, clouds, aurora borealis into the sky shader it became possible to limit the draw distance as close as you want. :D
Personally, I'm happy with the current clouds, but I'd also be happy to take another crack at improving their visuals further down the road. (e.g., multiple layers or styled volumetric clouds, something along those lines) The old cloud models were contr...
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