When pointing at a block that is under/behind water, the outline that indicates you point at that block is not visible.
The 2 screenshots show the expected behavior, not the bug.
I searched but couldn't find a similar report.
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Confirmed, but you better add some screenshots of the current behavior too. Your "expected behavior" screenshots actually show MC-9553 (hitbox rendered in front of water). The expected behavior would be "hitbox rendered behind water". The hitbox being completely invisible as of 13w42a is definitely a bug, maybe a side-effect of the inappropriate "fix" of MC-34649.
Btw., this happens with all transparent blocks, it's not restricted to water.
I didn't and I still don't see why the outline (hitbox) should be treated as a particle or as a part of the in-game world. The outline is there to show the player which block/object he/she is pointing at, its dimensions (hitbox), and which side exactly he/she is pointing at. It shows which block/object the player is about to interact with. It's a tool. It has a purpose and a function, it is not part of the world.
In other words, I don't see how hitbox being visible behind water could be included in MC-9553. Also for the reasons I explained above I consider what is depicted in "expected_behavior_1.png" and "expected_behavior_2.png" to be the expected behavior.
Also, what about generalizing this ticket to cover all the "not visible behind stained glass" things? (same happens with clouds as mentioned in MC-9553, also very similar to MC-35716). It's all more or less the same bug.
EDIT:
To summarize: The bug affects all transparent blocks (not restricted to water!), you can't see hitboxes, clouds and rain through them.
This was fixed in the 1.7-prerelease, can someone please resolve this?
Instead, hitboxes show MC-9553 again (rendered behind all transparent blocks as of 1.7)
Fixed in 1.7
Zombie hunter, it's only now that I understand what you meant. You are right, the outline is shown behind water in occasions where it should be drawn in front of it. And that is indeed an issue that belongs in MC-9553. It just hadn't occurred to me yet, so I misinterpreted your words. I'll upload a screenshot in your report.
Please, post some screenshots of the bug.