Dissolve the yeast in the 1/3 cup warm water and mix in two teaspoons sugar. Let the mixture sit for ten minutes, or until it thickens.
In a large bowl, whisk together the oil, salt, honey and sugar. Add ½ cup boiling water and whisk again to dissolve the sugar and salt. Add the cold water and whisk it in. In a medium bowl, whisk together the white whole wheat flour and the whole wheat and spelt flours.
Beat two eggs in a small bowl and add them to the oil mixture. Add the yeast mixture and mix it in well. Add one cup of the flour mixture and whisk it into the liquids. Add another cup of the flour mixture and use a wooden spoon, silicone spatula, or the dough hook of a stand mixer to mix it in. Add another cup of the flour and mix it in. Add the last ½ cup flour to the dough, and knead it into the dough until it’s mostly smooth. It can be a little sticky.
Sprinkle your counter with ½ tablespoon white whole-wheat flour. Remove the dough from the bowl and place on your dusted counter. To get all of the dough out of the bowl, scrape your fingers down the sides and gather the dough into a ball.
Sprinkle another ½ tablespoon flour on top of the dough. Wash the bowl. Add the remaining teaspoon of oil to the bowl and rub it around. Return the dough to the bowl, rub some oil on top of it and cover the bowl with plastic wrap. Let the dough rise for 2 hours.
While the dough is rising, prepare the filling. Place the chopped onions, poppy and caraway seeds, salt and oil into a small bowl and mix well. Cover and set aside until the dough has risen.
Divide dough in half, sprinkle some white whole-wheat flour on top of your counter.
Divide each half of the dough into three if making braided loaves and four if making a round basket weave. Roll each piece into a long strand, about 8 to 10 inches long. Use your hands to flatten the strand and stretch so that it is about 2 ½ to 3 inches wide. Use the side of your hand to press a trough into the center of the dough the long way. Scoop up a heaping tablespoon of onion mixture and spread along the dough into the indentation you made. Fold the dough over the filling and seal, creating a long rope. Set aside with the seam on the bottom while you prepare the other strands.
When all three strands are filled, braid them together and repeat for the second half of the dough.
If making the basket weave, place two strands horizontal with no more than an inch between them, and then the other two strands horizontally with one strand going over one vertical strand and the other going under the other vertical strand. Going clockwise, take each of the pairs of strands next to each other, if one had gone under the last strand, then place it over the next one; if it had gone over, then it should go under the next one. Repeat for the other three pairs. Repeat this again, with the strands going over or under the one next to it going in a circle around the loaf. Repeat again if your strands are long and then tuck the strands underneath and use your hands to shape it into a round basket. Repeat for the other four strands.
Place shapes loaves on the prepared cookie sheet or jelly-roll pan, leaving a few inches between them.
Let loaves rise for one hour. Preheat the oven to 350°F.
Brush the top and sides of the dough with the remaining egg, beaten with 1 teaspoon water. Divide the remaining onion mixture and sprinkle on top of the loaves. Bake for 30 minutes, or until the bread is golden.
