Textures which are stitched, such as the icons.png have overlapping textures.
Also some textures remove black outlines as if they were supposed to be transparent.
[Note: These are not issues caused by Client mods, or due to bigger textures]
Example Provided shows:
Hearts Overlapping
Connection Bar showing up in the Reticule.
Experience Bar missing it's black outline in game.
A Solution would be to make each texture it's own separate picture and load them where they should be constrained rather than overlap the edges of textures and remove the black borders in certain areas.
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Un-Modded Strictly Vanilla Minecraft, if you want to test it yourself just save the icons.png file and create a resourcepack with only that file and see for yourself
Is this still a concern in the current Minecraft version 1.7.4 / Launcher version 1.3.9 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
the issue is still present in the current version but more light has been shed on it, The hearts still overlap by 2 pixels in default textures but is seems that it might be intentional that the 32x32 image be overlapped with the one next to it to create a more solid bar which just means that the pictures are actually 30x32 with a cut off on one side.
the connection bar overlapping into the cross hair was a mistake made in up-scaling and was due to the fact the connection bar was 1 pixel to high which put it in the cross hairs selection range.
the black outline for the experience bar is still missing but that is not a huge deal, what is not a bigger issue is the transparent parts of the experience bar sometimes have a white background, as if MineCraft was not made to handle that portion with transparencies.
confirmed... have had this issue in 1.5 with texture packs. Air bubbles also seem to overlap even though the texutres are within the pictures original bounding box.