Heat the oven to 160°C / 320°F.
Heat the olive oil in a large Dutch oven over medium-high heat. Pat the short ribs dry and season all over with one teaspoon of sea salt and ½ teaspoon freshly ground black pepper. Sear on all sides until deeply browned, working in batches of 6 to 8 minutes so the pot isn't crowded. Transfer each batch to a large plate.
Reduce the heat to medium. Add the onion, carrots, celery, and peeled garlic cloves and cook until softened and fragrant, about 5 minutes.
Scrape the browned bits from the bottom of the pot with a wooden spoon. Add the tomato paste and stir. Cook, stirring occasionally, until it darkens and caramelizes, 2 to 3 minutes.
Return the short ribs to the pot. Add the red wine, broth, thyme, rosemary, bay leaf and chili flakes. Arrange the ribs meat-side down so they are fully submerged. Bring to a simmer, then cover and transfer to the oven.
Cook for 3 hours. Check the ribs — the meat should be tender and giving, but not yet falling off the bone.
Uncover and cook for a further 30 minutes to deepen the colour and reduce the sauce.
Discard the herb stems and bay leaf. Taste and adjust the salt. Serve with an extra pinch of chili flakes. See notes to thicken the sauce further.