This is a rookie follow up question to the question here: Need *.aux file in separate folder
The answer says:
"In MiKTeX you can additionally set --aux-directory=dir which will put only the auxiliary files in this directory."
How do I apply this --aux-directory=dir to MiKTeX? Do I put it in the preamble of my document? I can't get the interpreter to parse it.
Thanks! David
[Follow up from T.D.'s excellent answer]
T.D. - I use TeXShop, which is the normal Mac build I believe. I have put that code everywhere I can think of in the options, the most promising looking spots were in the screen below. Sadly, no love - it obstinately continues to put the aux files next to each of my .tex files (in all folders, which is what I'm trying to avoid).
Any TeXShop users have any ideas? Thanks!


pdflatex --aux-directory="dir" texfile– Feb 04 '15 at 15:41pdftex --aux-directory=auxfiles --file-line-error --synctex=1andpdflatex --aux-directory=auxfiles --file-line-error --synctex=1. I have a subdirectory in the same folder as the main.tex file I am compiling calledauxfiles, however it continues to put all the files in the root folder (and next to the .tex files in their respective subfolders). Any ideas? – – David Feb 05 '15 at 12:31