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pdflatex generates a lot of files that are of no use to me but are important to pdflatex (.aux, .fls, .log, .nav, .toc etc). How can I hide these files, e.g by putting them in some other, global directory? I don't want to see them when using LaTeX normally.

latexmk has the -auxdir option, but it only works with MiKTeX.

Tim N
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    Don't do this:-) Almost always when people do do it they end up coming back asking how to configure their editor, and latex and bibtex and biber and makeindex and.... to find the files they have hidden. However see http://tex.stackexchange.com/questions/7265/need-aux-file-in-separate-folder – David Carlisle Mar 04 '14 at 09:48

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