[MC-78647] Clouds make water invisible/Clouds render in front of water

When looking at water with clouds below the water, the clouds appear as if they were in front of the water, not behind it.

Environment

Windows 8.1, x64, 16 GB RAM, Intel Integrated Graphics, 2.5 GHz CPU, with "TurboBoost" to 3.5 GHz, Java Version 8 Update 40.

Also: Linux Mint Cinnamon Edition 17.1, 6 GB RAM, AMD/ATI Radeon HD 3200 Integrated Graphics, 2.4 GHz CPU, Java 8 Update 40.

Notice how the clouds appear to be above the waterfall, though they are actually below it.

Dupe of MC-9553

Another example.

Its already resolved as a duplicate. No need to update it.