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Slice the squash very thinly, ideally on a mandoline. Combine warm water and salt in a large bowl and add the sliced squash. Soak for 25 to 30 minutes, until soft and bendy. Drain squash, and press out as much water as you can; then lay out to dry.
Preheat oven to 450 degrees.
Coat a baking sheet or pizza pan with a thin layer of olive oil or a dusting of cornmeal. On a clean working surface dusted with flour, gently stretch the pizza dough to fit your pan, roughly a 10" x 6" rectangle.
In a large bowl, combine 2 tablespoons olive oil and several grinds of black pepper. Add the squash and toss to evenly coat. Layer the squash slices over pizza dough, leaving a crust.
Bake for 20 to 25 minutes, until the squash is tender and starting to turn golden brown. Remove from oven and top with mozzarella slices. Place back in the oven and bake until cheese melts, 5 to 10 minutes. Remove from oven, let cool slightly and top with baby arugula, a drizzle of balsamic and flaky sea salt. Cut into slices and serve.