In a large pot of salted water, bring to boil over high heat.
While waiting for the water, make the gremolata in a food processor: include 1/2 of the garlic (chopped roughly), parsley, and lemon zest until evenly combined. Season with salt. Scoop into a small bowl and set aside.
Heat remaining garlic and olive oil in a large, lidded (to prevent splatter) sauté pan over medium heat. Sauté garlic until aromatic but not yet coloring, about 2 minutes. Add onions and sauté until translucent, about 4 minutes. Stir in chili flakes.
Add spaghetti to boiling water and cook, according to package directions until just shy of al dente. Drain spaghetti, reserving 1 cup pasta water.
Meanwhile, lightly season onion mixture with salt. Increase heat to medium-high and add clams. Stir to coat shells and cover pan (preferably a glass cover so you can see the magic). Cook until clams just pop open, about 5 minutes. Uncover pan, remove from heat and discard any clams that remain tightly closed. Stir in half of gremolata.
Once spaghetti is boiled and drained, return clams to stove over medium-high heat. Once hot, add spaghetti, a few splashes reserved pasta water and butter, and toss to form a creamy sauce, about 1 minute. If pan looks dry, add water until sauce coats noodles. Off heat, toss in remaining gremolata and season with lemon juice and salt. Enjoy!