1. Preheat the oven to 350°F. Line 2 large shallow baking sheets with parchment paper.
2. Combine the flour, flax seed, wheat germ and cinnamon in a medium bowl. Whisk together the pumpkin, peanut butter, egg, sugar, water and oil in a separate bowl. Pour the wet ingredients into the dry and stir with a spoon or rubber spatula until a very rough dough forms. Knead the dough in the bowl until the dough comes together; it should be very slightly moist.
3. Turn the dough out onto a lightly floured work surface and roll out to a 1/4-inch thickness. With a 3-inch dog bone or cat shaped cookie cutter, cut out treats and transfer to the prepared baking sheet. Press all the scraps together, kneading once or twice, then roll out to 1/4-inch thickness and cut out more treats; repeat if necessary. Brush the top of each treat with the egg yolk.
4. Bake treats until lightly browned and fairly hard, rotating the pans from top to bottom once, about 35-40 minutes. Remove from the oven and cool completely; biscuits will harden as they cool. Store in an airtight container.