In a large bowl, whisk together flour, yeast and salt and set aside
Add the warm water, ¼ cup at a time, and mix with a spatula or your hands between each addition until a sticky dough forms
Add half the diced jalapeños and mix (see Note 2)
Use a spatula to fold the dough towards the center onto itself and away from the sides of the bowl, rotating as you fold (don't worry if it's super sticky)
Cover with a clean damp cloth, ensuring it's not touching the dough and rest until doubled in size (see Note 3)
Once dough has risen, preheat oven to 450℉ and place a Dutch oven inside
Leave the pot inside for 30 minutes (this is important because the dough needs to go into a hot pot)
Sprinkle a large surface with flour and cover your hands then turn the dough onto the surface
Cover with cheese and diced jalapeño then fold it over itself and repeat 2-3 times until the 2 cups of cheese is used; reserve ½ cup and sliced jalapeño (it doesn't have to be perfect, any cheese that falls out will get crispy on the crust; see Note 2)
Tuck the edges under by folding towards the center and flip the dough over so the smooth side faces up
Carefully remove the hot pot from the oven, place the dough over parchment paper, and add it to the pot (you can optionally score the top with an X, but you don't have to) Bake covered for 30 mins, then carefully uncover and sprinkle with ½ cup cheese and sliced jalapeño (see Note 4)
Bake uncovered for 10-15 mins or until golden brown (see Note 5)
Allow to cool for at least 45 minutes before slicing (see Note 6)