Combine cumin, peppercorns, coriander, cardamon, cloves, cinnamon, bay leaves and nutmeg in a spice grinder and work to a powder. Brush pork with 1 tablespoon olive oil and season well with spices, salt and some fresh thyme. Refrigerate about 1 hour.
Heat oven to 425º. Strew bottom of dutch oven with onion, carrots and garlic to create a bed for pork. Add cider. Set the pork shoulder, fat side up, over vegetables and cider and place in oven. Roast until top of meat is golden brown and crisp, about 40 minutes. Reduce heat to 300º, cover dutch oven and continue cooking another 6 hours. The meat should be very tender and easily fall from the bone. With about 1 1/2 hours left to go, halve and core fruit. Toss with remaining tablespoon olive oil, fresh thyme and a pinch of sea salt. Arrange apples, cut side up, on a parchment lined baking sheet. Place in oven (on a rack below meat) and roast until meat has finished cooking. Remove meat and apples from oven. Shred meat from bone and serve alongside apples.