Users, I am using LaTeX for homework at university. By now, I had always other programs generating some files, that I used in my LaTeX-document. For example MATLAB generated some graphs, Inkscape generated some pictures and so on.
I always used a folder structure like this:
/experiment01/matlab/ /experiment02/matlab/ /experiment02/inkscape/ ... /beamer-presentation01/ /beamer-presentation02/ ... /fulltext01/ /fulltext02/ ...
With this, I am on the one hand able to use figures again in different versions of presentations and the thesis text. On the other hand, my latex references break, if I rename folders. Also the old presentations do not have a fixed state, because the sketches done by Inkscape might change (if not versioned).
What do you recommend? Do you keep your proper work separated from the LaTeX-files? Do you refer to the same figure again in different documents or do you copy it?