After exporting your cookies (using some Export cookies Firefox add-on), you can use the following while-loop to backup your progress regularly into a a clean git repository.
while true ;
do \
curl -O -b cookies.txt \
http://substance.io/$USERNAME/$DOCUMENTNAME.latex ; \
git commit -asm"Auto-save." ; \
sleep 60 ; \
done
And thanks to _mql for getting back some lost lines.
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