Preheat the oven to 350°F. Line a baking sheet with parchment paper.
Make the flax egg: Add the water and ground flaxseed to a small bowl and stir well to combine. Let the mixture rest at room temperature for 15 minutes, until it has thickened and congealed.
Wet ingredients: To a large bowl, add the flax egg, applesauce, molasses, and vanilla extract. Stir well to combine.
Dry ingredients: Add the whole wheat pastry flour, spelt flour, light brown sugar, baking soda, ginger, cinnamon, nutmeg, and cloves to the bowl containing the wet ingredients. Stir well until the dry ingredients are evenly incorporated. Gently fold in the pear chunks.
Cut the scones: Transfer the dough to a lightly floured surface and shape it into a rough circle. Try to avoid flattening it out too much as you do so—the dough should stay thick and somewhat puffy. Use a sharp knife to cut the dough into 8 triangles.
Bake: Gently transfer the triangles to the prepared baking sheet, ensuring sufficient space between each triangle. If you want to sprinkle the tops with organic cane sugar, do so now. Bake the scones for 12 to 14 minutes, until they have puffed up and have some structure. They should still be somewhat soft when you remove them from the oven.
Cool: Let the scones cool on the baking sheet for 5 minutes. Then, transfer them to a cooling rack. Allow them to continue to cool until they are slightly warm or have reached room temperature. Enjoy as-is or with a mug of hot coffee or tea.