In a small cup or bowl, stir together the water and ground flaxseed and let sit until gelatinous, about 10 minutes; this will be the flax “eggs.”
Meanwhile, in a large bowl, combine the flour, sugar, cinnamon, cloves, baking soda, and salt, and whisk together. In a medium bowl, combine the ginger, vegan butter, agave nectar, vanilla, and vinegar, and whisk together. Add the flax “eggs” to the wet ingredients and whisk together well. Pour into the dry ingredients and stir together with a wooden spoon. Refrigerate for 1 hour.
Preheat the oven to 325°F. Grease two baking sheets with vegan butter or line with parchment paper.
Remove the chilled dough from the refrigerator. Using a 2-tbsp. measuring utensil, scoop the dough onto the prepared baking sheets, leaving enough space for the cookies to spread out as they bake. You should have eight or nine cookies on each sheet. Slightly flatten each mound to about 1 1⁄2 inches in diameter.
Bake the cookies until they have risen a bit and crackled on top, about 15 minutes. Remove them from the baking sheets and transfer to a wire rack. Let cool completely.
Store the cookies in an airtight container at room temperature for up to 8 days.