Preheat oven to 425 degrees F.
Slice onions into thin slices and add the them and 1 teaspoon salt to a large saucepan with 1 tbsp oil.
Cook slow and low for 10 minutes until the onions start to wilt, stirring occasionally.
Now you can make your pizza dough.
Combine 1 cup all-purpose flour with yeast, sugar and salt.
Then add the water and knead for one minute.
Gradually add the 3/4 cup of whole wheat flour and thyme and knead until you have a smooth ball (hehe) or about 3-4 minutes. Add more flour if needed.
Put dough aside. By now, your onions should be pretty soft. Add the honey and a little more olive oil if the onions are sticking. Sweat your onions for 5 more minutes and then add the tomatoes, thyme, red chili pepper flakes and more salt to taste.
Cook for an additional 5 minutes until the tomatoes start to cook and the onions are cooked down. You also want to make sure to cook away any moisture from the tomatoes so your hamantaschen are not soggy.
While your mixture is cooling a bit, roll out the dough very thin- about an 1/8 of an inch. Cut the dough into rounds using a 2 or 3 inch circle cutter (the top of a glass will due). Then put a teaspoon and a half of the filling in the middle of each circle.
Fold up the sides to form a triangle, making sure to securely pinch the ends closed.
Put the hamantaschen on a cooking sheet lined with parchment paper and sprinkled with cornmeal and bake at 425 for 5 minutes.
Then sprinkle on goat cheese and bake for another 5-7 minutes until your pizzas are golden brown and the cheese is bubbly.