For example, here are the steps for a TeXstudio user on Windows 10 with the latest MikTex who uses PdfLaTeX and BibTeX:
- Go to Options --> Configure TeXstudio.
- Under Commands, add
--aux-directory=poop to the PdfLaTeX line and poop/% -include-directory=poop to the BibTeX line. (I named my auxiliary folder poop. Replace poop according to your tastes, but be consistent.)
- Enable Show Advanced Options in the bottom lefthand corner.
- Go to the Build tab. Under the Additional Search Paths heading, you'll find a line for Log File. Add
%cd%\poop. This ensures that TeXstudio finds your log file in the auxiliary folder.
The next few steps are about a centralized bibliography maintained by Mendeley.
- Navigate to
C:\Program Files\MiKTeX\bibtex\bib\local. The local folder may not exist; create it in that case. You'll also want to make sure that Mendeley can actually write here. Right click the folder --> Properties --> Security. Change the permissions for Users: highlight Users, click Edit..., and check Full control.
- Update the filename database (FNDB) in MikTeX. Depending on which version you have, this could be located in different places. I found it under the 'Tasks' tab.
- In Mendeley, go to Tools --> Options --> BibTeX. Under BibTeX Syncing, change the path to
C:\Program Files\MiKTeX\bibtex\bib\local. You'll probably have to restart Mendeley before the .bib files show up there.
- Finally, to make sure that autocomplete still works, you have to tell TeXstudio where to find your amazing centralized directory. Go the Adv. Editor tab and find the Additional Search Paths section. In the Bib Files line, add
C:\Program Files\MiKTeX\bibtex\bib\local.
P.S. I had something strange happen with my BibTeX encoding along the way. I don't know if this is a universal problem. But under the Adv. Editor tab, find the Bibliography section. Make sure Parse BibTeX is checked and that the bib File encoding is set to System.
P.S.S. I think it also a good idea to save all these changes as a profile. Simply go to Options --> Save Profile.