How to make `latexmk` run the appropriate amount of times Does latexmk run pdflatex only once? If you run it another time, do you get an error All files are up to date? If yes, the problem is only related to auctex's log parser, not to latexmk.
How add dots in table of contents (list of papers) in combine class This sounds related as well (I don't know the combine class well enough to know if the techniques used in either question are usable here): tex.stackexchange.com/questions/112058/table-of-contents-for-set-of-pdf-files/
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