Prep: Combine the ground flax and water together in a small bowl; mix well, then set aside for at least 5 minutes.
Dry Ingredients: Whisk the flour, ginger, cinnamon, cloves, allspice, baking soda, and salt together in a medium bowl. Set aside.
Wet Ingredients: Add the butter and brown sugar to a large bowl. Use a handheld mixer (or standing mixer) to cream the butter for 3 to 5 minutes on low speed, scraping the sides of the bowl with a rubber spatula as necessary. Add the molasses, prepared flax “egg”, and vanilla to the bowl and beat again until smooth, about 1 minute.
Combine: Add the flour mixture to the wet ingredients and beat on low speed until combined, scraping the sides of the bowl as needed. The mixture should look crumbly once mixed, but will stick together when pressed with your hands.
Chill: Form the dough into one large ball, then cut in half. Flatten each half into a flat disc, then wrap in plastic wrap and refrigerate for at least 3 hours, preferably overnight. Chilling the dough is required for this recipe as it helps the flour to absorb extra moisture and prevents the cookies from spreading.
Baking Prep: Preheat the oven to 350F and line a large baking sheet with a silicone baking mat.
Roll: Cover a cutting board with an extra silicone mat (optional, but prevents sticking) and a light dusting of flour. Remove one dough disc from the fridge and use a rolling pin to roll out the dough until it’s about 1/4” thick. Sprinkle the dough and/or rolling pin with extra flour as needed to prevent sticking.
Cut the Cookies: Use cookie cutters to cut out your cookies; I find it works best to press down firmly, then wiggle the cutter a bit to fully separate the edges. Remove excess dough, then use a bench scraper or spatula to transfer the cookies to the baking sheet 1/2" apart from each other. You may need to use multiple baking sheets for each disc of cookie dough.
Bake: Bake in the middle rack of the oven for 8 minutes for soft cookies that are 4” or less. If your cookies are larger, bake for 10 to 11 minutes. If you prefer crunchy cookies, bake the cookies for a few minutes extra. Remove from the oven and let the cookies rest on the baking sheet for 10 minutes before transferring to a wire rack to let cool completely.
Repeat: Knead the dough scraps back together, and repeat steps 7-9 with both the scraps and the second disc of dough until all cookies have been baked. Try to roll out the dough as smooth as possible, as cracks will show in the final cookies (though they will still be tasty!). You can use your fingers to pinch the dough together when necessary.