Place the sauerkraut in a colander and rinse well under cold tap water. Squeeze dry.
Toss together the apple slices, flour and spices. Drizzle in the honey and mix well.
Saute the onions in the butter until clear and soft (5- 8 mnutes). Add the dry mustard and the sauerkraut, and cook another few minutes over medium heat. Remove from heat.
Take half the grated cheese, and combine it with the breadcrumbs and chopped nuts. Leave the other half of the grated cheese to stand alone.
In your buttered deep-dish casserole, make the following pattern of layers: 1st a layer consisting of half the apple mixture, next, half the onion-sauerkraut mixture; 3rd the plain grated cheese, 4th the remaining apples, followed by the remaining/sauerkraut mix, and FINALLY, the nut-crumb-cheese topping!
Cover and bake for 20 minutes and uncover and bake 20 minutes more.