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?
Setting up something like webui for storing those files for every paper, something like gitlab or gogs, could really help. It could add more transparency, ability to add some feedback in the issues, and so on.
I've had success using \import{subdir/}{BasenameInSubdir} from the import package.
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.
