In a large mixing bowl, toss the meat with 1½ teaspoons salt and ¾ teaspoon pepper.
Add 3 tablespoons oil to the insert of the IP. Set it to Sauté and let the oil warm up.
Meanwhile, peel and quarter the onion, then slice thinly crosswise.
Add the onion, cinnamon, ginger and nutmeg to the oil, along with ½ teaspoon salt and ¼ teaspoon pepper. Cook until soft, stirring occasionally, about 8-10 minutes.
Add 1 cup broth and use a spatula to scrape up all the brown bits at the bottom of the insert, then add the beef and 2 cups broth. Press Cancel/Keep Warm. Lock on the lid and make sure the release knob is in the seal position. Cook for 13 minutes.
Meanwhile, peel and chop the root vegetables into 1" cubes. Chop the prunes in half.
When the beef is done, immediately release the pressure. Press Cancel/Keep warm. Unlock and remove the lid. Add the vegetables prunes, then lock on the lid again, make sure the release knob is in the seal position, and cook for 2 minutes. Immediately release the pressure. Press Cancel/Keep Warm.
Taste and add more salt or pepper, if necessary. Serve in bowls and sprinkle with fresh thyme.