Prepare the crust by mixing flour and salt together in a large bowl. Using a pastry blender or fork, cut in cold butter until you have pea-sized pieces. Sprinkle water over the mixture one tbsp at a time and work the dough with your hands. Stop adding water when the dough starts to form large clumps. Continue mixing until the dough just comes together. Do not overwork, you should still be able to see specks of butter. Divide the dough in half, then wrap in plastic and chill for at least 30 minutes.
Chop broccoli into bite sized pieces. Chop green onion and grate cheese.
Add broccoli and green onion to a pan with butter and sauté on medium heat until broccoli is bright green and slightly tender, about 7 minutes. Remove from heat and set aside.
Preheat the oven to 177°C. Whisk together eggs and milk, seasoning generously with salt and pepper.
On a floured surface, roll both halves of the sprouted spelt pie crust to about ⅛" thick. Using a 4-4.5" round cookie cutter, cut out circles of dough. Re-roll scrapes until all of the dough is used. Place the dough circles in a clean* muffin tin, forming them gently to the bottom.
Using approximately half of the cheese, add a small amount to the bottom of each cup. Distribute broccoli mixture evenly through the cups, they should look about ½ to ¾ full. Pour egg mixture over the broccoli until the cup is about ¾ full (it's okay if there is some broccoli sticking out) and top with remaining cheese.
Bake for 25-30 minutes, until the egg is set and crust is lightly browned.