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It's very helpful to have the pdfs in one location, but it would be even better if the week and lecture number prefixed the title so they could be sorted. The following shell code is one way to do the renaming.
for w in 1 2 ; do
( cd week${w}
for n in 0* ; do
lnum=$(echo ${n} | cut -c 1-3)
lnam=$(echo ${n} | cut -c 4-)
( cd ../pdfs
git mv ${lnam}.pdf ${w}${lnum}-${lnam}.pdf )
done )
done
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