Whisk together both flours, baking powder, and baking soda.
In the bowl of a stand mixer fitted with a paddle attachment, beat the butter, both sugars, and the salt together on medium speed for 3 minutes, or until thoroughly blended; scrape the bowl as needed. Add the egg and beat for two minutes more.
Turn off the mixer, add the dry ingredients and mix only until combined. Add the cranberries, poppy seeds, and chocolate and mix again until just combined. Scrape the bowl to bring the dough together. Line a baking sheet with parchment. Divide the dough into 15 pieces, roll each piece into a ball between your palms and place on the baking sheet. Cover the balls and refrigerate overnight.
Adjust an oven rack to the middle position and preheat the oven to 425F [220C]. Line a baking sheet with parchment paper. Keeping the remaining balls of dough in the refrigerator until needed, arrange 8 cookies on the sheet, leaving 2 in [5 cm] between them. Sprinkle each cookie with a little flaky sea salt, crushing it between your fingers as you do.
Bake the cookies for 10 minutes, then pull the baking sheet from the oven and, using a metal spatula, the bottom of a glass, or the back of a spoon, tap each cookie lightly but smartly – you want to deflate a bit of the cookie and leave an indentation. Let the cookies rest on the baking sheet for 3 minutes, then carefully transfer them to a rack. Repeat with the remaining dough, using a cool baking sheet.
The cookies are ready for munching after they’ve cooled for about 10 minutes, or you can wait until they reach room temperature. These are best eaten the day they are baked and really best shortly after they come from the oven. But they’re still way above average even 3 days later; keep them in an airtight container.