Preheat oven to 350F degrees. Add the olive oil to a large skillet over medium-high heat. Stir in the cumin, chile flakes, paprika, salt, onion, and garlic. Cook until onions soften, just a minute or two. Stir in the chopped tomatoes and cook until the tomatoes soften up a bit, another two or three minutes. Set aside.
Take six pieces (quarters) of the pita bread, gently open each of them and tuck them into the muffin tin - every other slot. If the pita splits, no worries, just criss-cross the bread into a nest or tart shell of sorts so there is coverage across the bottom so the egg and filling won't run out.
Spoon a bit of the tomato filling into each pita cup, dividing it amongst the six cups. Now crack a single egg into each pita cup. You don't want the cups to overflow, hold back a bit of the egg white if you need to. Also, you don't want the egg yolk to jet up toward the sky, try to ensure it is level with the whites or the yolks can dry out while baking.
Carefully place in the oven (racks in the center) and bake for about 15 minutes. Until the whites have set and become opaque. Serve hot garnished with a sprinkling of chopped tomatoes, chile flakes, and/or a bit cilantro.