How can Bibtex find the auxiliary files it needs when these are stored in a subdirectory

Question

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?

Answer 1

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

./auxfiles/$basename

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.