I'm sure the guys won't mind me jumping in here, but for anyone that is getting the "black sky during day" problem *and* they are using SH3Cmdr and JSGME, try this FIRST:
1. Perform a rollback in SH3Cmdr.
2. Disable the Atmosphere mod in JSGME.
3. Re-enable the Atmosphere mod in JSGME.
This combination of steps "cleans" your SH3 files. And, as a number of people have already attested, it has worked for them with this and many other mods.
To avoid similar file problems with *any* mod in the future, ALWAYS rollback SH3Cmdr BEFORE installing/enabling new mods. Whilst usually not a problem, it is always a good habit to get into to ensure that you limit the potential for file clashes.
Also note that you can adjust water density via SH3Cmdr in conjunction with running this mod without causing side effects.
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