Cairo-dock, the graphical shell I use on the concerned computer is shown over the window while playing on the snapshot, when Minecraft is in focus, which obscures the hotbar, and everything on the lower window if Minecraft is maximised.
This did not occur in 1.5.1 (As you can see in the third screenshot. The same is also true in 1.5.2), Where Cairo-dock is correctly hidden behind the game window when the Minecraft window is over it, this is also true in fullscreen.
LWJGL is the same on both versions, as you can see in the second two screenshots, so this is not the issue, as has been previously suggested.
Steps to Reproduce:
1. Start launcher (new dev launcher, not old) by locating it and right clicking, selecting Oracle Java.
2. Select relevant snapshot.
3. click 'Play'.
4. Maximise window if not already (but not F11 fullscreen, the problem does not occur then).
5. The issue becomes apparent: exactly as it appears in the screenshot of the snapshot, cairo-dock is shown over the lower part of the game, when the game is in focus, and the window area is over the dock.
To summarise
Torabi sums it up very well (far better than I can, at any rate):
So, to summarize: The Minecraft window should cover (be on top of) the dock when the Minecraft window has focus. This is the behavior it had in 1.5.1.
The problem being experienced is that the dock is always on top of the Minecraft window, regardless of focus.
Screenshots
1. (2013-04-25 18_27_27) Screenshot In snapshot with issue
2. (2013-04-25 20_31_19) Screenshot showing the version of LWJGL for the snapshot
3. (2013-04-25 20_33_01) Screenshot showing version of LWJGL in 1.5.1, and that the issue does not occur in 1.5.1
Edited to clarify many points, thanks, Torabi
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Version of LWJGL used on both my copies of 1.5.1 minecraft and the snapshot is 2.9.0 (confirmed with console on both, I can provide screenshots if it's really necessary), same issue still occurs, so this issue is /not/ invalid, and it's definitely not nothing you can solve.
Attached screenshots, you may noticed that the snapshot minecraft window is not in focus, but I can assure you that the issue still exists when it is, and I can prove this too if you wish...
Also, I can appreciate that you have to deal with invalid issues on a daily basis, but you really shouldn't dismiss something such as this out of hand.
lemakje,
korikiisulda
I notice that the issue clone I created has been trashed, is anyone prepared to offer an explanation for that, or why this issue is being disregarded?
korikisulda, refer to screenshots by their names, not by order, as the order may change (especially if new screenshots are added).
So this is actually a window layering/stacking/z-order issue, and not a bounds/fullscreen issue. That may be something Mojang could actually control.
So, to summarize: The Minecraft window should cover (be on top of) the dock when the Minecraft window has focus. This is the behavior it had in 1.5.1.
The problem being experienced is that the dock is always on top of the Minecraft window, regardless of focus.
That sums it up perfectly, and now the issue is vaguely presentable, thanks so much Torabi, you really should be a mod here.
One more question: what about the launcher window? If you move that down so that it overlaps with the dock, which is on top?
The old launcher (and the game itself, up to 1.5.1) uses javaw. The new one is a native application, and I've read that it launches the game client with java. This may not seem like a big difference, and theoretically, it shouldn't be – but it might have some effect on window layering on some systems.
Not sure what we can do about this. Seems to me that LWJGL must somehow know the limits until where it can expand on linux.
This is nothing we can solve. Please report to LWJGL. https://github.com/LWJGL/lwjgl/issues