Heat 1 tablespoon of the oil in a Dutch oven or ovenproof stewpot, and sauté the onion, carrot, garlic, and thyme over medium heat until browned, 8 to 10 minutes. When the vegetables are nicely colored, transfer them to a bowl. Wipe out any little bits of vegetable clinging to the pan so they don't burn when you sear the beef. Pat the meat cubes dry and season them with 1/2 teaspoon of the salt and 1/4 teaspoon of the pepper. Add 1/2 tablespoon of the oil to the pan and sear the beef in batches over high heat until it is a rich mahogany brown on all sides. This will take approximately 5 to 7 minutes depending on the thickness of the meat. Cubes tightly packed in the pan won't brown properly. Clean out any juices which are released before the next batch. Over high heat add 1/2 tablespoon of oil for each batch, then sauté the meat until browned on all sides. Preheat the oven to 375 degrees F. Return the vegetables and the meat to the pan, dust the meat and vegetables with the flour, and cook for 2 minutes over medium heat, stirring frequently. Toasting the flour helps to develop the overall flavor of the stew. Add 3 cups of the red wine to cover the beef and bring to a boil. Add the tomato and season the stew with the rest of the salt and pepper. Cover the stew with a round of parchment paper or the lid slightly ajar, place it in the oven; and cook for 1 1/2 hours, or until the meat is tender. (If as the stew simmers the wine reduces below the meat, add a little water.) While the stew cooks, bring a medium pot of water to a boil. To peel the pearl onions, trim the roots and make a small X with a paring knife in the other end. Boil the onions for 3 minutes, spoon them out, and set them aside to cool. Then squeeze the onions out of their skins. In the same water, blanch the bacon pieces for 3 to 4 minutes, and drain. Heat a medium skillet, add the remaining oil, and brown the bacon and onions. Add the mushrooms and cook over high heat until golden brown. Pour off any excess fat, add the final cup of red wine to the vegetables, and simmer until the onions are tender, about 10 minutes. When the beef is tender, remove the stew from the oven, stir in the vegetables, and simmer for 10 more minutes. Pour the stew into a warm bowl, dust with the minced parsley, and serve with buttered noodles.