Preheat oven to 350F. Line 2 large baking sheets with parchment paper.
In a small bowl, whisk together the ground flax seeds and water. Set aside and let it thicken for a few minutes.
Meanwhile, add your butter and brown sugar to a medium mixing bowl or the bowl of a stand mixer. Beat the sugar and butter together with the stand mixer or a hand mixer. You can also use a fork and whisk it manually if you prefer. Add the molasses, flax egg and vanilla. whisk until creamy.
In a large bowl, combine the flour, cinnamon, ginger, nutmeg, clove, baking soda and salt. Transfer the dry mixture to the wet mixture and stir to combine. The mixture will seem dry, this is normal.
Place the dough on a lightly floured surface. Knead a few times until the dough becomes smooth. Roll it out using a rolling pin, until it gets about 1/4-inch thick.
Cut the dough using a cookie cutter. Transfer the cookies to the prepared baking sheet. Form another ball using the leftover dough, roll it out again and form more cookies. Continue this process until all the dough is used.
Bake for 8-10 minutes. The cookies should be slightly crispy around the edges and soft in the middle. They will get crispier as they sit. Let them cool completely.