In the bowl of a stand mixer, whisk together flour and yeast, then add salt. With mixer on low, slowly add water, mixing for about 1 minute. Raise the speed to medium (4 on a KitchenAid) and continue mixing for 7 minutes. The dough should clean the sides of the bowl, but still be soft and elastic. If it sticks to the sides, add additional tablespoon of flour. (By hand, work the dough in the bowl with wet hands, scooping and stretching for about 10 minutes until smooth and springy.)
Scrape dough into a bowl lightly coated with oil or cooking spray. Flip so that all surfaces are oiled, then cover with plastic wrap and let rise in a warm place until doubled, about 1 1/2 to 2 hours.
Cover a baking sheet with parchment paper and oil or spray with cooking spray.
Scrape risen dough onto a well-floured counter and cut into 6 equal pieces. Using well-floured hands, shape each piece into a ball by forming it over your middle finger and pulling dough down and around, pinching closed at the bottom, forming a smooth top. Place on baking sheet, flour the tops, then cover with plastic wrap and a clean dish towel. Let rise for about 1 hour, or until slightly puffy.
In the meantime, heat oil in saucepan, then add onions, sautéing about 5 minutes, or until soft and translucent. Off heat, stir in poppy seeds and salt. Set aside.
Preheat oven to 450 degrees at least 30 minutes before baking.