In a bowl, dissolve the fresh yeast in lukewarm water.
Add the whole wheat flour, sugar, and salt. Stir in the yeast mixture, olive oil, and egg yolk. Knead for 8-10 minutes until smooth, shape into a ball, cover, and let rise for 45 minutes.
While the dough rises, cut the bell pepper and zucchini into thin strips. Slice the fresh tomatoes. Finely chop the garlic. Cut the shallot into thin rings. Roughly chop the thyme.
Heat roughly 2 tablespoons olive oil in a pan over medium heat. Sauté the garlic and shallot rings for 1-2 minutes. Add the bell pepper and zucchini strips and cook for 1-2 minutes more. Remove from heat and set aside. Preheat the oven to 180°C (356°F) with top and bottom heat.
Roll the dough to 3 mm thick and place on a baking sheet lined with baking paper. Spread the sautéed vegetables on top. Arrange the fresh tomato slices and halved dried tomatoes over the vegetables. Scatter the thyme and oregano over everything.
Season with salt and pepper. Drizzle with olive oil. Bake for 30 minutes at 180°C (356°F). Scatter the flaked almonds on top and bake for 5 more minutes.