Place 1/2 cup warm water in a large bowl, stir in sugar, then sprinkle on yeast and stir to dissolve. Set aside.
Place yogurt and one cup water in a saucepan, stir to mix, then place over medium heat, stirring occasionally, until lukewarm.
Add the yogurt mixture to the yeast and water mixture and stir. Add the whole wheat flour one cup at a time, stirring in one direction only as you add the flour then stir for about one minute in the same direction to activate the gluten. Let this sponge stand, covered, for 10 minutes or for as long as 2 hours.
Sprinkle 1 tablespoon salt over the sponge, then stir in unbleached flour one cup at a time until dough is too stiff to stir. Turn it out onto a lightly floured surface and knead for 10 minutes, until the dough becomes smooth and elastic, incorporating more unbleached flour as necessary to prevent dough from sticking.
Rinse out, wipe and lightly oil your bread bowl. Add the dough, cover with plastic wrap, and let rise until doubled in volume, approximately 1 1/2 hours.
Position a rack in the top third of your oven. Arrange unglazed quarry tiles on it, leaving a 1-inch gap between tiles and the oven walls (to allow air to circulate). (Alternatively place a baking stone or baking sheets on the rack).
Preheat the oven to 500 degrees F. Gently punch down the dough and turn out onto a lightly floured surface and let rest, covered, for 10 minutes.
Place shallots and remaining salt beside your work surface, together with a bowl of lukewarm water. Divide dough into 8 equal pieces. Using lightly floured hands, press each piece into a 4-inch round.
Work with one round at a time, leaving the others covered at the back of your work surface. Working on a lightly floured surface, roll out to a 6-inch round.
With a fork or bread stamp, or the edge of a wire whisk, stamp a 1 1/2-inch diameter circle at the center of the bread thoroughly, to flatten and pierce it (to prevent it from rising). Sprinkle onto the center approximately 1/2 teaspoon chopped shallot, a pinch of salt, and a sprinkle of water.
Quickly roll out and prepare one, two, or three more breads (depending on the size of your oven), then transfer prepared breads to the hot tiles, stone, or baking sheets.
Begin shaping your next breads as the first batch is baking. Let bake for approximately 7-8 minutes, or until lightly golden.
Use a long-handled peel (or spatula) to remove from the oven. Place on a rack to cool, then stack and wrap loosely in a cotton cloth to keep soft and warm. Shape and bake remaining breads in the same way.