The runs start when you gain your crosshair (escape_02) and end when you interact with the toilet in the relaxation chamber (Chamber 0).
After the end of the game you will have to open the developer console and type this:
crosshair 1
the reason behind this is that I wanted to mimic the ending of the original Portal game.
It didn't quite work out so I had to come up with a different solution to disable the crosshair at the end.
So I made the player type "crosshair 0" into their consoles without them knowing (hammer thing) and it doesnt reset to crosshair 1 after you decide to replay the mod.