- In heavy large wide pot, heat oil over medium-high heat. Season beef with salt and pepper. Add beef to hot oil in pot and cook until lightly browned all over, about 3 minutes per side. Transfer beef to bowl.
- Add lardons and cook until lardons release fat and become golden, about 5 minutes. Transfer lardons to bowl and set aside. Add onions to lardon renderings and sauté for about 5 minutes, or until tender without any color.
- Form bouquet garnish from rosemary, sage, thyme and bay leaves. Form sachet with juniper berries and cloves. Add sachet, bouquet, sugar, and garlic to onion mixture. Return beef to pot, add stout, wine, and vinegar and bring to a simmer.
- Cover and braise in 275°F oven for about 4 hours, or until meat begins to fall off bone. Spoon off excess fat. Discard bouquet and sachet.
- In large saucepan, melt butter over medium heat. Whisk in flour and cook, stirring often until mixture has the texture of sand and is golden brown.
- Gradually whisk braising liquid into roux to form gravy.
- Meanwhile, remove any bones and cartilage from meat. Pull meat into large meaty morsels. Stir gravy into braised meat, onions, and lardons. Bring to a simmer. Simmer until mixture thickens slightly.
- Season with salt and pepper and a splash of vinegar, if desired. Cool completely.
- Position rack on lowest rung of oven and set baking sheet on rack. Preheat oven to 400°F. (Being close to source of heat will help bottom crusts bake and brown properly.)
- Unwrap larger disk of dough, set it on a floured surface, and lightly dust top of dough. Roll out dough into a 13-inch round, occasionally rotating dough and dusting it with flour to prevent sticking. Brush away excess flour and transfer dough to a 9-inch glass pie plate, centering it in pie plate and letting excess dough hang over the edges. Lightly press dough into dish. Refrigerate pie shell.
- On floured surface, roll out other disk of dough into a 12-inch round.
- Transfer enough of beef mixture to pie shell to fill (reserve any remaining filling for another use). Arrange second dough round over filling. Trim dough overhang to 3/4 inch. Pinch crusts together and fold overhang under.
- In small bowl, whisk egg and milk to blend. Using pastry brush, lightly brush top of pie with egg-milk mixture. Sprinkle with flaky salt and freshly ground pepper.
- Place pie on preheated baking sheet in oven and bake for 40 minutes, or until crust is deep golden and filling is bubbling. If crust begins to brown before filling bubbles, tent pie with foil. Let pie cool on a wire rack until warm before serving.
- Cut pie into wedges and serve.
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