Make the pasta dough:
Knead together all ingredients until the dough is smooth. Let rest 1 hour.
Make the filling:
- In a skillet over medium-low heat, sauté shallots and garlic until tender. Remove from heat.
- In a bowl, mix all filling ingredients except garnishes and chill for 1 hour.
- On a pasta machine, gradually roll out dough to thinnest setting. Using a teaspoon, spoon out filling onto middle of dough, spaced 1 inch apart. Brush water on top half of pasta and lay over bottom half. Seal with your fingers, making sure there are no air bubbles. Place on a baking sheet with flour and keep chilled until ready to cook.
- Bring a stockpot of salted water to a boil. Cook pasta for 1 to 2 minutes. Strain and serve topped with olive oil, lemon zest, and smoked almonds. (The agnolotti is also great tossed in browned butter and parsley.)