The pastry dough can be made up to 2 days in advance, or up to right after the beef goes into the oven—just be sure to give it an hour in the fridge to chill.
Put the flour, salt, sugar and thyme leaves in a food processor and pulse until the thyme is finely minced.
Drop in the butter and pulse about 10 times, until the mix resembles wet sand and most of the butter is cut down to the size of peas (though don’t worry if some pieces are larger).
Mix the water and vinegar in a small liquid measuring cup and, with the processor running now, pour in the water. You want it to be just moist enough to hold together.
Turn it out onto a lightly floured surface, form it into a ball, roll into a disc, and cover tightly with plastic wrap before stashing in the fridge.
Preheat your oven to 300°
Tumble the pancetta or bacon in a Dutch oven and place over medium heat. Once they start to sizzle a little and their fat begins to ooze out, reduce the heat to low and continue to cook, stirring occasionally, until they’re crisped and all the fat has been rendered.
Remove the pork from the pan with a slotted spoon to a paper towel lined plate and set aside. Also, pour the fat from the pan into a heat-safe bowl and set aside—DO NOT DISCARD!
Toss the beef with about 1 ½ t-spoons of the salt. Place the Dutch oven back over medium heat and, once hot, add in 1 tablespoon of the reserved pork fat with ½ tablespoon of butter, and sear the beef. Do this in batches—about 3 or 4 for this amount of beef—keeping the pieces from touching as much as possible so you get a good sear on them. If the fat in the pan begins to burn, remove it and refresh with new fat from your reserve. The same goes for if the pan starts to get a little dry.
Once the beef is seared, remove the fat and discard. Add another tablespoon of butter, and half that of pork fat. Drop in the onion, cut side down, along with the carrots. Leave them for a few minutes—what you’re going for hear is a slight sear on the onions. Once you’re there, lower the heat and add in the thyme, garlic, tomato paste and bay leaves. Stir to melt the tomato paste and cook the garlic—just a minute or two.
Pour in the brandy and deglaze the pan, scraping up any brown bits that have stuck to the pan. Pour in the wine and beef stock and add the beef and pancetta/bacon back to the pan. If the beef isn’t just covered, add a little more stock.
Bring it to a simmer, cover the pan, and place in the oven for 2 ½ - 3 hours, until the beef is tender.
About 15 minutes before the beef comes out of the oven, heat 1 tablespoon of butter with 1 – 2 t-spoons of the bacon fat (or olive oil, if you’re out) in a large sauté pan until hot and sizzling. Drop in the pearl onions and cook about 10 minutes, until caramelized. Drop in the mushrooms and toss to combine, cooking another 5 minutes or so until they too take on a caramel color.
Turn the oven up to 350°
Remove the beef from the oven, and remove the onion, carrot, and bay leaves from the pot and discard them. Bring the liquid back up to a boil while you mash a tablespoon of butter into a tablespoon of flour in a small dish. Once the liquid is boiling, drop the mash into the pot and whisk to combine. Let it bubble for a few minutes more, then turn the heat to low and simmer for a few minutes until the stew is thick and luscious. Stir the pearl onions and mushrooms into the stew and check for seasoning.
Divide the dough into six equal sized pieces and roll them out on a floured surface so that they are just slightly larger than the diameter of your bowls. Beat the egg with the water until very well combined.
Distribute the stew equally among six 10-ounce oven safe bowls. Brush a little of the egg wash around the lip of each bowl and lay the dough over the top of the stew, folding it down onto the side of the bowl just slightly. Cut a few slits in the top of the crust to allow the steam to escape. Brush the pastry with the egg wash before sprinkling them with coarse, flaky sea salt.
Bake for about 40 minutes, until the crust is golden brown and the stew piping hot. Let them rest out of the oven for about 5 minutes if you can stand it before diving in.