Preheat oven to 400°F.
Prepare pasta according to package directions. Drain. Set aside.
Place 2 tablespoons butter in a large pan. Place over medium heat and melt butter.
When butter is hot, add shallots. Cook until light golden.
Sprinkle shallot butter mixture with flour. Cook, stirring often, 1 minute.
Add wine. Stir, picking up any browned bits from the bottom of the pan. Add cream. Stir well.
Sprinkle in Gruyère and Gouda cheeses, a small bit at a time, stirring until each addition is mostly melted before adding the next.
Stir in 2 tablespoons chives, mustard, 1/4 teaspoon salt, cayenne and nutmeg.
Stir prepared pasta into cheese mixture.
Pour mixture into a 2 quart baking dish.
In a food processor, pulse bread with remaining 1 1/2 tablespoons butter, 1/2 tablespoon chives and 1/4 teaspoon salt until coarse bread crumbs form. Sprinkle bread crumbs over pasta and cheese.
Place dish in preheated oven. Bake until top is browned and cheese is bubbling.
Remove from oven and serve hot.