The latexpand perl script, the flatten and flatex programs. Please upload your papers in the future! :)

https://tex.stackexchange.com/questions/21838/replace-inputf...

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.

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.