Preheat the oven to 350 degrees.
Line two baking sheets with parchment paper or silicone mats.
Whisk the flour and baking soda together in a mixing bowl. Set aside.
In the bowl of a stand mixer, cream together the butter and sugars. I like to beat them together for about three minutes to add some air to the batter.
Mix in the eggs, one at a time. I never remember to take out the eggs, so I let them sit in a bowl of really warm water until I get to this step.
Add the vanilla and mix. Make sure you are scraping the sides and bottom of the bowl with a spatula from time-to-time.
Mix in the pure pumpkin puree. It make look curdled during this step, but don't worry.
Add the cinnamon, nutmeg, and ground cloves to the batter.
Add the flour and baking soda to the batter and mix everything together. Again, make sure you scrape the side and bottom of the bowl.
Stir in the chocolate chips using a spoon or spatula. If you are not using the chocolate wafers, you can add a bit more than 1/2 cup.
Scoop the batter onto the prepared trays. I use a small cookie scoop, but you can use a tablespoon. Leave room between the cookies for spreading.
Chop the semisweet chocolate bar into small pieces.
Press a few pieces of chopped chocolate into the top of each cookie.
If you are using the salt - either fleur de del or sea salt - top a little pinch onto the top of each cookie before baking. Oddly, if you do this from a bit high up, it will work out better than holding your hand right over the cookie.
Bake for seven minutes, then rotate the trays.
The cookies are done when they are golden, about 13-15 minutes total.