Yesterday (Sep. 1, 2016) I ran all of the automatic updates for my MiKTeX. Since then, my TeXworks has not been writing .log or .aux files, at least not in the same directory as my .tex file or anywhere that I can think to look. Naturally this a problem since I search these files for warnings, missing character messages, multiply-defined labels, etc. Is there anything I can do to try to fix this problem? I'm using TeXworks Version 0.6.1 (MiKTeX 2.9) [r.3614278, 5/1/2016 4:43 AM], and my computer is Windows 7.
Even a file as simple as
\documentclass{article}
\begin{document}
\section{Test}\label{sec1}
Reference to section \ref{sec1}.
Reference to section \ref{sec2}.
\end{document}
produces, in its directory, only a .pdf file and a .synctex.gz file. Oddly, the \ref{sec1} command prints correctly as "1". The \ref{sec2} command prints as "??", obviously, but since I have no .log file I have no way of confirming that the paper has undefined references.
EDIT: I'm also set up to run normal LaTeX on a .tex file via DVIWindo, and DVIWindo seems to have "seen" all the appropriate MiKTeX updates I made; the updated files are being used, and the .aux and .log files are still being written as normal.
Best Answer
Okay, I just now (Sep. 9, 2016) followed the instructions in the answer to this question to find the "--clean" option and remove it. It was under pdfLaTeX+MakeIndex+BibTeX. Now my TeXworks is writing all the files it should. If this is enough, thanks for your help.