The next day, remove the meat from the marinade and then pat dry with a kitchen towel.
Strain the marinade and discard the vegetables and herbs, reserving the liquid.
Transfer the liquid into a saucepan and simmer for 5 minutes over low-medium heat.
Skim the scum from the top of the liquid now and then, making sure it's all clear and keep aside to add later to the stew.
Preheat the oven to 170° C (340° F) and heat your Dutch oven or oven-safe heavy-based pan on medium to high heat, and put the oil in.
Fry the meat in the pan in three batches until nicely browned on all sides. Make sure your pan is hot enough before adding the meat as we need a quick caramelization. Don’t put the meat all together in one batch as a large amount of cold meat will cool the pan down and will stop the caramelization.
Transfer the meat onto a plate and then use the same pan to brown your vegetables.
Turn the heat down to medium and then add more oil to the pan if needed. Add the diced onions and then sauté for a few minutes.
Add the carrot and garlic and then sauté for a few more minutes.
Gently brown the vegetables for 5 minutes, and stir in the flour along with the tomato paste and black pepper.
Add button onions (or shallots) and return the meat to the pan. I like my button onions nicely cooked and soft so I add them to the stew at this stage. However, if you like your button onions crispy, skip adding them to the stew at this stage and add them with the garnishes.
Mix well and add some of the wine from the marinade. Deglaze the pan, and add the rest of the wine, beef stock (just enough to cover the meat), thyme, and bay leaves.
Bring it to a boil, cover it with a lid or tin foil, and put the Dutch oven in the preheated oven. The cooking time depends on the type and size of the meat. I usually check after 2 hours and after that every half an hour until the meat is tender and falling apart easily when touched with a fork.
45 minutes before the end of the cooking time, start preparing your garnishes.