Preheat oven to 350 degrees. In a heatproof bowl soak the porcini in the water for 15 minutes. Drain the porcini, reserving the liquid, pat dry and chop fine. Strain reserved soaking liquid through a double thickness of dampened cheesecloth into a bowl.
In a skillet set over moderate heat cook the onion in the butter, stirring occasionally, for 5 minutes.
Add the spinach, garlic and mushrooms and cook, stirring, 3 to 4 minutes, or until heated through. Transfer mixture to a bowl, add remaining ingredients (using only 1/2 cup of locatelli) and gently stir to combine well.
Cook the manicotti in boiling salted water until just al dente. With a slotted spoon transfer to a bowl of cold water, drain and pat dry. Gently stuff shells with filling and arrange in a buttered baking dish.
Make the sauce: In a saucepan set over moderately low heat melt the butter, add the flour and cook the mixture, whisking, for 2 minutes. Add the milk and reserved mushroom liquid and bring to a simmer, whisking. Add nutmeg, salt and pepper and simmer, whisking occasionally, for 5 minutes.
Spoon the sauce over the manicotti, sprinkle with the remaining locatelli and bake, covered with foil for 30 minutes. Uncover and bake for 10-15 minutes longer. Let rest 5 minutes. Sprinkle with snipped fresh chives.