I know that this issue has been around for a long time, but I would like to make a note of it in the official bug tracker.
Clouds still pass through solid objects in their path, instead of becoming transparent. I've heard that Mojang is reworking the rendering engine for Minecraft and it would be nice if they finally fixed this issue.
I've attached a gif I have seen around multiple sites, most likely coming from this: http://www.reddit.com/r/Minecraft/comments/e7xol/this_is_how_clouds_should_work_gif_simulation/
I don't know if that method would work, but it would be nice to get someone at Mojang talking or thinking about this issue again.
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This is a feature request, not a bug.
You can request features over at the minecraft forums
Hardly a feature. Just poor programming. I highly doubt clouds are meant to pass through solid walls and buildings. If so, whoever came up with this as a "wise" idea was a fool. Obviously shortsided on someone's part in never expecting skyscrapers or sky cities to be built. I am at odds to why modders can fix these issues in a matter of days, yet the core team can't fix something like this in years (back when Notch decided that this was a good idea and should be fixed).
I hear the argument that it would add to CPU "strain" but obviously stars, sun, and moon circle around the world but don't travel through skyscrapers and high structures. The question is why clouds couldn't be inserted into the minecraft stratosphere where stars reside.
Is this still a concern in the current Minecraft version 1.6.4 / Launcher version 1.2.5 ? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
Technically not a bug, but a feature request, but I like it. Would love to see this in the game. Doesn't look like it would take too much computing either.