Rough Directory Structure:
cmp/
computing files (programmatic modelling/data analysis)
res/
static resources (data, images, external outputs, etc.)
tex/
LaTeX source for paper (everything for the final PDF)
src/
source folders
out/
output folders
Try to keep everything clean and organized;
graph/image renders from code in cmp/
should go in res/
...
similarly, src/
of tex/
should reference files in res/
(do not duplicate resources)