Yes, this bug is annoying. A nice thing to have would be to be able to
specify extra command-line options for the tools involved. As a
workaround, I have

#!/bin/sh
/usr/bin/pdflatex -synctex=1 $@

in ~/bin/pdflatex

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https://bugs.launchpad.net/bugs/414431

Title:
  rubber does not support synctex

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