Move presource patches out of work/

I forgot we had a clean command in the paper util

scripts/init.sh

@@ -19,7 +19,7 @@ fi
 # apply patches directly to the file tree
 # used to fix issues from upstream source repos
 cd $basedir
-prepatchesdir="$workdir/pre-source-patches"
+prepatchesdir="$basedir/scripts/pre-source-patches"
 for file in $(ls $prepatchesdir)
 do
     if [ $file == "README.md" ]; then