Run right out of the stick house and into the forest. When you arrive at the blocking bushes, throw a bomb and roll through.
As you approach the metal door with the Holy Cross etching on it, type in the code (DRULUR) to open the door. Inside, open the left-most chest for mana berries (3). Exit the room.
Walk to the ladder to the left and Ladder Storage off of the bottom. Run SW, split the columns by the opening warp pad, and continue to the Atoll loading zone. As soon as the next scene loads, quit and continue. Save in Atoll.
At some point in the run (before Librarian boss), you need to trigger the code for a free ice bomb. This can be done anywhere in the run, but I'll put a note here because I've found it convenient to do here.