1. In a large mixing bowl, combine the flour, yeast, sugar, and salt.
2. Add the warm water and ¼ cup of olive oil. Mix until a dough forms.
3. Knead the dough on a floured surface for about 10 minutes until smooth and elastic.
4. Place the dough in a greased bowl, cover, and let rise in a warm place for about 1 hour or until doubled in size.
5. Preheat the oven to 425°F (220°C).
6. In a skillet, heat 2 tablespoon of olive oil over medium heat. Add the sliced onions and cook until caramelized, about 10 minutes.
7. Punch down the dough and spread it out on a greased baking sheet. Use your fingers to make dimples in the dough.
8. Spread the caramelized onions over the dough. Sprinkle with fresh thyme leaves and coarse sea salt.
9. Bake for 20-25 minutes or until golden brown.
10. Let cool slightly before slicing and serving.