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1
Stir together yeast, 1 teaspoon brown sugar, and warm water in a large bowl and let stand until foamy, 5 to 8 minutes. (If mixture doesn't foam, start over with new yeast.) In a separate bowl, stir remaining 2 tablespoons brown sugar into warm milk until dissolved.
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2
Add 2 1/2 cups flour and milk mixture to yeast mixture and stir with a wooden spoon or rubber spatula until a soft dough forms, adding up to 1/2 cup additional flour, a little at a time, if necessary. Turn out dough onto a lightly floured surface and gently knead a few times to form a smooth ball. Transfer to a clean bowl. Cover with plastic wrap and let rise in a draft-free place at warm room temperature until doubled and bubbles appear on surface, about 2 hours.
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3
Preheat oven to 400u00b0F with rack in upper and lower thirds. Line two 4-sided sheet pans with parchment paper.
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4
Turn out dough onto a lightly floured surface and cut into 4 equal pieces. Lightly dust your hands with flour, then gently roll and stretch 1 piece of dough to form a 12-inch-long rope. Flatten dough and arrange so a long side is nearest you, then roll out to a roughly 12- by 4-inch rectangle with a lightly floured rolling pin. Gently press one fourth of ham and cheese into lower third of rectangle, leaving a 1/2-inch border along bottom edge. Stretch bottom edge of dough up over filling and press tightly to seal, then roll up as tightly as possible to form a rope. Cut rope into 12 pieces and transfer to a sheet pan. Make 3 more ropes with remaining dough, ham, and cheese and cut into pieces, transferring to sheet pans. Let rest at room temperature, uncovered, 30 minutes (dough will rise slightly).
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5
Bring water (6 cups) to a boil in a 4-to 5-quart saucepan. Reduce heat and stir in baking soda. Cook pretzel bites in batches in gently simmering water, turning once, until slightly puffed, about 20 seconds. Transfer with a slotted spoon to sheet pans.
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6
Bake until puffed and golden-brown, about 15 minutes (cheese may ooze slightly).
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7
Meanwhile, stir together mustard, jalapenos, and honey.
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8
Brush warm pretzel bites with butter and sprinkle with pretzel salt. Serve warm or at room temperature with jalapeno mustard for dipping.
