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I am using Blender 2.78c and trying to make a tree. When I decide the size, shape, variation of my tree, I add the leaves. Everything looks fine, but when I add the leaf material, the leaves get detached from the branch and some leaves go through the branch.

Did I miss something or the Sapling addon is not polished?

enter image description here

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When you created your leaf from a plane, the planes origin default to dead center. Sapling assumes your leaf's origins is at the base of the stem. Since your origin is in the center, you'll get the misplaced leaves shown in your image. To fix this. - Put Focus on plane/Leaf - Set "Pivot Point" (it's found at the bottom of your blender screen" to "3D Cursor"
- Click your cursor to bottom of the leaf stalk - On left side of screen, select "Set Origin" >> "Origin to 3D Cursor".

That should take care of your problem.

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