In a large bowl, stir together the yeast, sugar, and warm water. Let it sit for 10 minutes. It should look foamy and smell yeasty.
Pour in the apple cider vinegar, olive oil, half of the flour, and salt. Mix with a fork in the bowl, then add the remaining flour and knead on the counter once it gets too thick. Gently knead until all flour is combined and the dough is smooth.
Grease the large bowl with some olive oil, place the dough ball in, cover with a towel and let it rise in a warm place for about 1 hour to 1 hour and 15 minutes. A cold oven is a great place for this to avoid drafts.
Once the dough has risen, oil a square (8x8" or 9x9") metal baking dish and place the dough inside. Use your fingers to spread and dimple the dough, then cover with a towel and let it rise for another 30-45 minutes. With 15 minutes remaining, preheat the oven to 500ºF. Ensure you remove the dish if the dough was rising in the oven!
Once risen, spread the cheese over the dough to the edges of the pan. Yes, cheese first! Then top with diagonal lines of marinara sauce and pepperoni slices.
Bake for approximately 25 minutes on the bottom rack (the lowest it will go), depending on your desired level of crispiness. Yes, the edges of the cheese may burn slightly, but that's okay.
Remove from the oven, and run a knife along the edges to loosen the pizza from the pan. Use a spatula to help remove the pizza, then use a sharp knife to slice into 4 squares. Top with a drizzle of honey, chili flakes, and dried oregano. Enjoy immediately!