Make the bechamel: Place onion and butter in a medium saucepan over medium heat, and cook until onion is translucent and softened, about 5 minutes. Add flour, and cook, stirring constantly, for 2 minutes. Whisk in milk in a slow, steady stream. Cook, stirring constantly, until mixture has thickened, about 5 minutes. Add 1 cup Gruyere, and stir until cheese melts. Remove from heat, add nutmeg, and season with salt and pepper.
To assemble: Heat oil in a large saute pan over medium heat. Add garlic, and cook, stirring occasionally, until softened, about 2 minutes. Add spinach, and cook, stirring occasionally, until wilted, about 2 minutes. Add red-pepper flakes, and season with salt, pepper, and a squeeze of lemon. Let cool slightly. Squeeze out any excess liquid, and coarsely chop.
Preheat oven to 450 degrees. Reserve 2 tablespoons of bechamel. Mix remaining bechamel and spinach in a medium bowl. Butter a rimmed baking sheet. Place 1 crepe on center of sheet, and top with 3 tablespoons spinach mixture, spreading evenly. Top with another crepe, then 3 tablespoons spinach mixture. Repeat with remaining crepes and spinach mixture, ending with a crepe. Spread reserved bechamel on top, and sprinkle with remaining cup cheese. Bake until cheese melts and turns golden brown, 10 to 12 minutes. Let cool slightly, then transfer gateau de crepes to a platter. Cut into wedges, and serve warm.