The problem I face is that my papers is in multiple tex files in several folders connected to a main.tex using \includes. Is there a convenient option that will take care of this issue?
https://tex.stackexchange.com/questions/21838/replace-inputf...
The basic (and unfortunate in a xkcd/1479 way) issue appears to be that the arXiv compile server doesn't allow writing to subdirectories. A subdir \include implicitly requires write access for the aux file.