Aenra, I meant there's a file on my Scales downloads page that just contains the crafting additions and nothing else.
Abraxas, I have some code I used for my mod, and looking into if it's possible to integrate it into main, which appears to be compatible still. First off, I have to disable existing atmosphere triggers, which is possible but a bit tedious (basically I'm giving them a negative height in the lsb files so they can't be entered. Then I'll add huge atmosphere triggers that covers the whole map of Cyseal, Luculla, Hiberheim, etc.
Now there's a few ways to do it I think to minimize transition issues. First off, there could just be 4 or 5 (dawn, morning, afternoon, dusk, night) atmospheres for each major area that transition very quickly every 4 minutes or so. Would still give a kind of impression of day-night, but damn is watching the atmospheres slowly transition into each other so much cooler. Problem with slow transitions is going to a new level or new area (e.g., underground) automatically finishes them. So something Sniper did was make 24 different atmospheres that slowly transition into each other. This way when an atmosphere gets finished from teleporting into them, the atmosphere will only be still for a moment. But that's more work and more difficult to work with for scripts probably (but not impossible.)
Another possibility is to keep existing atmosphere triggers and make 4-5 atmospheres for each so certain areas (like the burning area and foggy undead area) would maintain their vibe but there'd still be day-night cycles. But that's even more work and probably even more possibility for issues.
It's probably just the kind of thing you'd have to accept a bit of imperfection with, some situations not working exactly right but the overall effect still being pretty cool. I should probably finish Scales first, too...