It seems that parse_log.sh has moved from /path/to/caffe/scripts/ to /path/to/caffe/tools/extra. The edit changes the description to reflect this change. Nothing major really.
# You had better check the data files before designing your own plots.
# Please generate the neccessary data files with
-# /path/to/caffe/scripts/parse_log.sh before plotting.
+# /path/to/caffe/tools/extra/parse_log.sh before plotting.
# Example usage:
# ./parse_log.sh mnist.log
# Now you have mnist.log.train and mnist.log.test.