I had no troubles with arXiv in the past, if I could export my file(s) to .tex and compile them on my linux PC, the same worked with them.
If you're exporting for pdflatex, make sure you upload figures as pdf.
They accept .bib files, or at least they used to, no need for special prep. as in the case of am. phys. soc. journals that was discussed here recently.

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