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I have a tex file that has its biblography at the bottom of the article, but ArXiv does not like that and demands a bbl file. Is there an easy way to copy paste the bibitem objects into one of these files without having to completely change the format?

e.g. \bibitem[Landau et al.(1992)]{1992A&A...259..696L} Landau, R., Grasdalen, G., \& Sloan, G.~C.\ 1992, \aap, 259, 696

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    Mhhh, I always thought the arXiv liked it when the bibliography was added directly at the end with thebibliography. That is standard procedure and avoids all the .bbl malarkey that is normally necessary to upload to the arXiv (since they don't run BibTeX/process .bib files). Can you show us what your document looks like and what exactly the arXiv complains about? – moewe Feb 21 at 10:34
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    The first error is ! LaTeX Error: Option clash for package hyperref. and has little to do with citations. (See for example tex.stackexchange.com/q/329461/35864). Note also that currently your .bbl file is missing the \begin{thebibliography}{9}...\end{thebibliography}. There are also errors about the figures. – moewe Feb 21 at 12:41
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It sounds like you created the thebibliography environment by hand. If this assumption is correct, and assuming further that your main tex file is called main.tex, you should

  • copy all material in main.tex between \begin{thebibliography}{} and \end{thebibliography} into a file called main.bbl. (You may have to create this file from scratch; and

  • replace the copied material in the main tex file with the single instruction

    \input{main.bbl}
    

where main should correspond to the filename of your main tex file.

If you then rerun LaTeX on your main tex file, the output should be exactly the same.

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