Cook the bacon in a pot until fat comes out and the bacon turn light to medium brown. Remove the bacon and half of the fat. Put in a bowl. Set aside.Continue to heat the pot with bacon fat. Add the cubed beef and then cook for 5 to 8 minutes (or until the color turns medium brown) while stirring. Transfer to a bowl and include the juice. Set aside.Pour the bacon fat saved in step 1 into the pot. Heat the pot and then add the carrot; sauté for 3 minutes. Add the diced yellow onion. Continue to sauté until the onion gets soft.Put the cooked beef (with juice) and bacon back in the pot. Stir.Pour the red wine and beef broth. Let boil.Stir and add tomato paste and fresh thyme. Cover, set the heat to low, and then cook for 2 hours; add more beef broth if it starts to dry out.Meanwhile, melt the butter in a pan. Sauté the mushrooms in medium heat for 3 to 4 minutes; set aside.Put the pearl onions in. Cook for 8 minutes.Add the sautéed mushrooms with butter. Stir.Add salt and pepper to taste.Sprinkle the flour on top. Quickly stir until the flour completely dilutes in the sauce.Serve.