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Some publishers' system only compiles submitted .tex files in a single pdflatex or latex run, without running bibtex — hence the instruction to authors who used BibTeX during manuscript preparation to paste the contents of the .bbl file input into the .tex for submission. Here’s how you can do this on Overleaf:

  1. When all the content writing is done and ready to be submitted, click on the downward-pointing triangle next to “Download as Zip”, at the bottom of the project’s file list (in the leftmost panel).
  2. Click on either the “For submission to arXiV” option or the “Input and output file” option.
  3. When the .zip file has completed downloading, unzip it. You should find the .bbl file in there.
  4. Open the .bbl file with a plain text editor, and copy everything in this file.
  5. Back in your .tex file on Overleaf, comment out the line \bibliography. And in its place, paste the contents of the .bbl file that was copied just now.

The project is now ready to be submitted to the journal, complying with their requirement that the contents of the .bbl file are pasted in the .tex manuscript as one single file.