Melt the 8-ounces of chocolate + oil in the microwave (in 30 second increments on High, but microwaves are funky so keep an eye on things) in a large microwave-safe bowl or in a double boiler. Stir the chocolate to get rid of any chunks. Sometimes it will look chunky, but if you give it 20 or so stirs with a wooden spoon, you’ll get rid of all of the chunks without overheating (burning) it. Let cool slightly and then whisk in your eggs, brown + granulated sugars and vanilla extract.
In another bowl whisk together the rye flour, bread flour, all-purpose flour, cocoa powder, sea salt, baking powder and baking soda. Pour the flour mixture into the chocolate mixture and give a couple of stirs until the dough is just starting to come together. Add the cherries and mix until just barely combined. Lay some plastic wrap on the counter, dump the dough on top and wrap tightly. Chill the cookie dough for 20-30 minutes in the fridge.
Preheat your oven to 375 degrees F, place a rack in the top third of your oven (this is where you’ll bake your chocolate cherry cookies) and line your baking sheets with parchment paper or a silpat.
Gently roll 1 tablespoon of dough into a ball and place on the cookie sheet allowing about two inches between each dough ball. Bake for 9 minutes. You want to slightly under bake these. Once out of the oven sprinkle with the sea salt flakes (if using) and allow the chocolate cherry cookies to cool on the sheet for 5 minutes then transfer to a cooling rack.