Season short rips with salt and pepper. Heat olive oil in a dutch oven or 5 qt pot over medium-high heat. Add short ribs and sear all sides until they begin to brown. Set aside.

Add onion, carrots and celery to dutch oven and sauté until fragrant. Add tomato paste and stir until vegetables are coated, then add wine, lower heat to low and simmer for about 5 minutes.

Add beef broth, tomatoes, and red pepper flakes; stir to combine. Return short ribs to the dutch oven and ensure they are fully submerged. Place bay leaves and thyme sprigs in the dutch oven, ensuring they are submerged in the liquid.

Cover and simmer on low for 2-3 hours or until the beef can be pulled apart easily with a fork. Shred the beef and mix back into the cooking liquid.

Pre-heat oven to 400 degrees. Place spaghetti squash halves on a baking sheet, flesh side up, and rub with olive oil and spices if desired. Bake for 35 minutes and shred with a fork.

Serve ragu on top of spaghetti squash and garnish with parsley if desired.