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You can still maintain your usual file structure and continue working on Overleaf without modifying your existing source code. Just provide an extra main.tex file in the Project's top level, and use the import package to pull in the real main file in the subfolder:

  • Project Top Level
    • main.tex
    • paper/
      • manuscript.tex
      • refs.bib
      • appendix.tex
    • output/
      • chart.png
      • results-table.tex

Contents of main.tex:

\RequirePackage{import}
\import{paper/}{manuscript.tex}

The original \inludegraphics, \input etc in manuscript.tex would continue to work with respect to your project file structure.

You can find an example in action in the Gallery here.