I did [something similar] too when I started my PhD ... I had one Makefile managed project that ran everything with dependencies. From raw data, to figures and

I did [something similar] too when I started my PhD ... I had one Makefile managed project that ran everything with dependencies. From raw data, to figures and even embedding the numbers into the final, Latex-based PDF. My supervisor manually copied all of the text from my PDF into a word document on his first revision ...