This is meant to be helpful, and is according to my understanding of the directions, but it makes the most sense to me based on the watchdogs we must look for and after getting some input from Cheyenne.
I'm going to try to hopefully clarify this for a lot of people, based on my own understanding of the project. You should not actually explicitly declare a start or end node in your stagetext file. (do not place ! or . in your stagetext file, Menzies only uses this to make his matrices a little clearer while he's describing how they work). When you copy the explicit program into a stagetext format, most people are copying node for node the contents of the program as stage text. The problem with this is the program itself is flawed, which is why we're trying to fix it.
You should have a start node, with which no other node connects back to, and when you analyze your matrix, it should be the ONLY empty COLUMN in the Adjacency matrix.
You should also have an end node, and this node should not connect back to ANYTHING else in the program. It's adjacency matrix should have an empty ROW, and should be the ONLY empty row.