This is the defacto standard way of operating it I understand, which is mostly just hacking at stuff in small chunks until it sort of works and leaving comments

This is the defacto standard way of operating it I understand, which is mostly just hacking at stuff in small chunks until it sort of works and leaving comments throughout it with "run this bit on Tuesdays only". I recently had to inherit someone's R stuff and I had to learn R and fix it all. It now runs from a makefile repeatably. Anyway it could be worse. It could be Minitab.