Let the beef chuck roast sit in room temperature for 30 minutes to an hour. Dust generously with salt and pepper. Sprinkle flour over the chuck roast and pat to coat.
Turn oven to 275 degrees. Heat canola oil in a large Dutch oven until shimmering over medium-high heat. Cook the roast until it browns on one side, about five to eight minutes. Carefully flip and brown on the other side. Remove from the Dutch oven.
Lower heat to medium. Add garlic and cook for 30 seconds, stirring constantly. Pour in apple cider, beef stock and tomato paste, scrapping with a wooden spoon to loosen the brown bits from the beef. Add the thyme sprigs, rosemary sprigs, sage sprigs, cinnamon sticks, most of the onion slices, whole cloves and crushed red pepper to the Dutch oven. Place chuck roast back in the Dutch oven and the remaining onion slices on top of the roast.
Tuck in the petite potatoes and carrot chunks on the side of the roast. They don't need to fully submerge in the juice.
Bring braising liquid to a boil. Turn off heat, cover and place in 275-degree oven. Cook for a few hours until the meat easily shreds with a fork. A 3-pound roast should take three hours, a 3 ½-pound roast should take three and a half hours, and a 4-pound roast should take four hours, but judge doneness based on whether the meat is fork tender. If it's not easily shreddable, it needs more cooking time.
For the gravy, melt butter over medium heat in a skillet. Whisk in flour and cook for about three minutes, whisking constantly. Slowly pour in the strained pan drippings from the pot roast. Whisk until smooth. Add a pinch of salt and continue to cook until thickened. This should take a few minutes. Serve roast, carrots, potatoes and onions with gravy. Enjoy!