In a bowl, whisk the flour with the salt. Using a pastry cutter, cut the butter into the flour until the mixture resembles coarse meal. Drizzle the water over the flour and stir gently until just incorporated. Gently press to form dough. Flatten the dough into a disc, wrap in plastic and refrigerate at least 1 hour.. In a large fry pan over medium heat, warm the oil. Add the onions and cook, stirring occasionally, until the onions are golden brown, about 30 minutes. Transfer to a large bowl and let the filling cool to room temperature.. In the same pan, heat the oil over medium heat. Add the apples and sugar and stir to coat apples. Cook, stirring, until the apples are just starting to caramelize and have softened, about 8 to 10 minutes. Transfer to the bowl with the onions and stir in the cheese, chives, thyme, and salt and pepper to taste.. Heat oven to 425 degrees. Remove dough from refrigerator and let stand for 5 minutes before rolling out. Roll out the dough on a lightly floured surface to a 16-inch diameter. Transfer the dough to a cookie sheet lined with parchment paper.. Place the onion-apple mixture in the center of the dough. Spread to 1 ½ inches from the edge. Fold the edges of the dough over so that a small circle of filling is still showing in the center of the tart.. Place in oven on middle rack. Bake the tart for 10 minutes, then reduce heat to 350 degrees and bake an additional 15 to 20 minutes, or until the crust is golden brown. Remove from oven and let sit 10 minutes before serving.