Defining -aux-directory for pdflatex breaks citations for natbib

Question

When I run pdflatex with an -aux-directory flag it makes it so natbib can't find the citations.

pdflatex command with -aux-directory:

pdflatex.exe -synctex=1 -interaction=nonstopmode %.tex -aux-directory=auxillary

and without:

pdflatex.exe -synctex=1 -interaction=nonstopmode %.tex

When I run it with -aux-directory, no bbl file is generated, the references page is missing, and the log shows a long sequence of errors like the following:

Package natbib Warning: Citation `Altman2006' on page 1 undefined on input line

When I run it without -aux-directory, then everything is fine.

Has anyone else experienced this problem?

MWE:

PhD_Thesis.tex

documentclass[11pt,twoside,a4paper]{article}

usepackage[round,authoryear]{natbib}
begin{document}

Bibtex test: citet{Card1999}

bibliographystyle{apalike}  
bibliography{PhD_Bibliography}
end{document}

PhD_Bibliography.bib

@INCOLLECTION{Card1999,
    author = {David Card},
    title = {The Causal Effects of Education on Earnings},
    booktitle = {Handbook of Labour Economics},
    year = {1999},
    editor = {O. Ashenfelter and David Card},
    volume = {3},
    pages = {1801-1863},
    publisher = {Elsevier Science B.V},
    chapter = {30}
}

luneart · Answer

If your thesis is a single file (which is somehow unlikely) it is enough to append your bibtex command with ./auxillary/%.

Else, I've written a bash script shared in this answer but it's for linux environments. However you can copy the working in a bat file for windows:

first, the script needs to go into the aux folder
run bibtex on the main aux
copy the generated bbl file to all chapter filenames (eg main.bbl, chapter1.bbl, etc)

That's it, call the script instead of bibtex. Also, (that probably isn't a problem with -aux-directory, but one with -output-directory) if each chapter is in its own dedicated folder, you need to copy the folder structure into the build folder (here 'auxilliary').

Defining -aux-directory for pdflatex breaks citations for natbib

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