I recently moved to a new computer and have noticed that since installing the latest version of Miktex, compiling my documents no longer produces any auxiliary files whatsoever. The files that I used to see but are no longer generated are the .aux files, .bbl files (for BibTex), .log files, .out files, .thm files and .toc files. There is nothing other than the .pdf and synctex.gz file.
Despite this the pdf displays as usual. This would not bother me otherwise, but I can no longer upload to the arxiv no longer works correctly due to the missing auxiliary files. I am wondering if there is a way to force MikTex to produce the missing files.