1. Heat oil in a small skillet over medium heat. Cook onions and garlic, stirring, until brown and soft (5-8 minutes).
2. In a medium bowl, whisk together the onions, garlic, flours, active dry yeast, salt, and nutritional yeast.
3. Stir in the milk and water until the dough forms ball.
4. Cover the bowl with plastic wrap or a damp towel and let rise in a warm room (around 70 degrees F) for 12-15 hours.
5. After the dough has risen, scrape it out of the bowl and onto a lightly floured surface. Fold it a couple of times, then shape into a round loaf. Place loaf on parchment paper and return to your bowl, again covering bowl with plastic wrap or a damp towel. Let rise until doubled in volume (1-2 hours). (Cooler temps need longer proof times.)
6. While the dough is almost done proofing, place a large, heavy-bottomed, oven-proof, lidded pan in oven and preheat to 400 degrees F (20 minutes).
7. When dough is done proofing and oven is hot, score the top of the loaf deeply with a very sharp knife. Transfer onto parchment paper, place in preheated pan, and cover. Bake until loaf reaches an internal temperature of 195 degrees F (50 minutes), keeping the oven closed during the full bake time.
8. Remove from the pan and let cool for at least 1 hour before cutting and serving, warm or cool.