Look at the Off Hand in the pictures. This bug affects with Normal Map, Ocean Explorer Map and Woodland Explorer Map.
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I include the fix. By add GlStateManager.tryBlendFuncSeparate(SRC_ALPHA, ONE_MINUS_SRC_ALPHA, ONE, ZERO) to reset default blend state.
All class and mapping are based on latest MCP for 1.12.2.
I don't see the issue. Could you elaborate what part of the skin is going transparent?