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In order to make my major folder containing my master .tex file more clean, I have set Texworks to store all auiliary files in a subfolder called auxfiles. This was done by adding the following command line -aux-directory=./auxfiles into the Arguments list for the pdfLaTex processing tool in TexWorks (detailed explanation given in: How can I put .aux files in separate folder using a command inside TexWorks?). However, after having done this BibTEx is no longer able to find the auxiliary files it needs. How do I make BibTex find the auxiliary files it needs, and in addition put its output into the auxfiles directory?

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Did you try with ./auxfiles/$basename as the argument for the BibTeX engine? What operating system are you using? – egreg Feb 27 '12 at 21:32
@egreg Thanks a lot! It works fine : ) – Espen Donali Feb 28 '12 at 10:21
up vote 3 down vote accepted

You can modify the action of the BibTeX engine in the preferences of TeXworks, so that the argument line is


instead of simply $basename.

However, I suggest you to duplicate the engines: one normal BibTeX and another one, say BibTeX-AUX, that is modified in this way. Thus you'll be able to use both approaches.

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