To prepare the beef brisket, in a bowl, make a brine by combining the water, 4 ounces kosher salt, granulated sugar and 2 ounces of the liquid smoke. Stir to dissolve the salt and sugar. Cover and refrigerate until ready to use. 

Cut the beef brisket in half. Remove the fat, if desired. Inject the brine into the meat as much as possible. Place the beef in a large bowl and pour the remaining brine over the meat. Cover and refrigerate overnight. 

In a small bowl, make a glaze by combining the molasses, soy sauce and the remaining 1 ounce liquid smoke. Whisk until blended. Cover and refrigerate.  

In another bowl, make a spice rub by combining the 1 cup kosher salt, brown sugar, pepper, chile powder, paprika, dry mustard, onion powder and granulated garlic. Stir until blended. Transfer to an airtight container and store at room temperature.

Prepare a sous vide immersion circulator for use according to the manufacturer's instructions. Preheat the water to 154°F. Alternatively, use a closely monitored pot of water.

Remove the beef from the brine; discard the brine. Generously brush the beef on all sides with the glaze. 
Using a vacuum sealer, vacuum seal the individual pieces of beef according to the manufacturer’s instructions. Cook the beef sous vide at 154°F for 24 hours, checking every few hours to ensure the seals on the vacuum bags are still secure.

Preheat the oven to 425°F.

Open the bags of beef, reserving any rendered jus. Generously glaze the beef again and season heavily on all sides with the spice rub. Place the beef on a rack in a roasting pan, transfer to the oven and roast until the meat is well caramelized. Remove the beef from the oven and refrigerate.

To prepare the tomato puree, preheat the oven to 450°F.

In a large bowl, toss the tomatoes with 1/2 cup of the olive oil and the Cajun spice rub. Transfer to a baking sheet and roast until the skins have blistered and the tomatoes have started releasing their juices. 

Meanwhile, in a heavy pot over medium heat, warm the remaining 1/4 cup olive oil. Add the onion and garlic cloves and cook, stirring occasionally, until the onion is soft and translucent. Add the wine and deglaze the pan, stirring to scrape up the browned bits. Cook until the wine is reduced by three-fourths. Add the roasted tomatoes and rendered juices and the bay leaf. Reduce the heat to low and cook, stirring occasionally, until the tomatoes have completely broken down, about 2 hours. Remove and discard the bay leaf. 

Working in batches, transfer the tomato mixture to a blender and puree. Alternatively, using an immersion blender, puree the mixture directly in the pot. Strain the tomato puree through a fine-mesh sieve into a bowl. Season to taste with salt and pepper.

To prepare the basil essence, pour the oils into a blender and add the basil. Blend until smooth, using the plunger if necessary.  

Transfer the basil puree to a small stainless-steel saucepan, place over medium heat and cook, stirring constantly, until the puree is “army green,” 10 to 15 minutes.

Strain the cooked oil through coffee filters overnight. DO NOT PRESS OR SQUEEZE.

To prepare the filling, in a large bowl, combine the brisket, cheeses, sous vide liquid, glaze, egg, parsley and chives. Mix well by hand. Season with spice rub, salt and pepper. Transfer the filing to a piping bag with a small opening.

In a large stockpot over high heat, bring salted water to a boil. 

To form the agnolotti, cut the pasta lengthwise into 3-inch-wide strips. In a small bowl, whisk together the eggs and 2 tablespoons water. Brush the edges of the pasta with the egg wash, then place 1-tablespoon mounds of the brisket filling down the length of the pasta, spacing the mounds 3 inches apart. Fold the top of the pasta down to the bottom and pinch closed. Press the dough flat between the mounds of filling. Using a pastry cutter, cut half-moons, using the folded part as the flat side of the moon. Repeat with the remaining pasta and filling. Let the agnolotti stand for 5 to 10 minutes to set up before cooking. 

Turn down the boiling water to a heavy simmer and cook the agnolotti until tender.

Gently toss the hot cooked agnolotti with the tomato puree. Sprinkle with the dry jack cheese, drizzle with the basil essence and serve.