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I am using WinEdt 10.3 with the LaTeXify macro for easy use of Biber.

I am compiling my documents with pdfLaTeX and have set a folder for pdfLaTeX temporary files elsewhere on my disk:

--aux-directory="C:\Users\User\Github\MSc_Thesis\parts\tmp"

When this option is set, Biber cannot be run. Can I pass an option to Biber to notify it of the different path, or solve this problem some other way?

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    you could try to set up an auxiliary folder in options->executions modes->tex options. Perhaps winedt then takes care of the pathes. But I never tried it, I dislike auxiliary folders, imho they make to much trouble. Life is much easier when everything is one folder. – Ulrike Fischer Feb 21 at 12:23
  • Is there then any good way to clean up the temporary files after pdfLaTeX has successfully run? Was unable to find something so far. – Wasserwaage Feb 21 at 12:26
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    winedt has menu entry: tools->erase output files. But I use it only if I get errors that needs a removal. – Ulrike Fischer Feb 21 at 12:43
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Biber's option --output-directory may help you here.

From Biber's --help output

--output-directory [directory]
    Output files (including log files) are output to directory instead
    of the current directory. Input files are also looked for in
    directory before current directory (but after "--input_directory" if
    that is specified).

for completeness

--input-directory [directory]
    .bcf and data files will be looked for first in the directory. See
    the biber PDF documentation for the other possibilities and how this
    interacts with the "--output_directory" option.

Indeed

pdflatex --aux-directory="C:\Users\User\Github\MSc_Thesis\parts\tmp" test
biber --output-directory="C:\Users\User\Github\MSc_Thesis\parts\tmp" test
pdflatex --aux-directory="C:\Users\User\Github\MSc_Thesis\parts\tmp" test
pdflatex --aux-directory="C:\Users\User\Github\MSc_Thesis\parts\tmp" test

(or rather its equivalent on my PC) produces the expected PDF for me (here test.tex is a small test document that cites a few entries from a .bib file in the same folder).

But please let me reiterate that build folders like this often cause more problems than they do good. All programs involved in compiling your files need to support such an aux directory and need to be configured to know about it. (I'm not sure for example about the various indexing tools and their capabilities of dealing with aux directories.)

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