Place the beef pieces in a bowl or plastic bag and sprinkle with flour and a few grinds of pepper; toss to coat evenly but lightly.
Heat the cooking oil in a large Dutch oven over medium-high heat and brown the beef in batches, ensuring not to crowd the pan; turn pieces to brown all sides, about five minutes per batch, then transfer to a plate.
Reduce the heat to medium and add onions, garlic, red chili pepper, leek, celery, carrots, and dried thyme (if using); cook and stir for a couple of minutes to loosen the browned bits on the bottom.
Pour in the red wine to deglaze the pan, scraping up all flavorful residues.
Return the browned beef to the pot along with any juices; add the beef stock, diced tomatoes, kosher salt, and freshly ground pepper; stir well.
Cover the pot, bring the mixture to a gentle boil over medium heat, then immediately reduce the heat to low to maintain a slow simmer.
Sprinkle fresh thyme (if using) and fresh parsley over the stew; add the bay leaf and cover the pot again.
Let the stew simmer gently for approximately two hours, stirring occasionally to prevent sticking.
Taste and adjust seasoning 15 to 20 minutes before serving to ensure balanced flavors.
Serve the stew hot over plain boiled potatoes for a simple, rustic meal.