Textures are shaded with the assumption that lighting is coming from the top, but for tools, when used in-hand, the texture is flipped, and the lighting seems to be coming from the ground.

Attatched is a resourcepack that proposes a simple fix. May not work so well with asymetrical items like axes, but works perfectly for swords and pickaxes. (I whipped this up in a minute, so it only works for diamond swords in the main hand)