Clean up SDCard. I normally scan my photos with JPG because it's much faster to load. And I will make changes, delete bad ones, during the scan. In the end, I want the corresponding CR2 whose JPG counterparts have been removed being cleaned. This script does the job.

sd-dedup.sh

#!/bin/sh
set -e

cd /Volumes/CANON/DCIM/100CANON;
for f in *.CR2
do
    b=$(basename $f .CR2)
    if [ ! -f "/Volumes/CANON/DCIM/100CANON/$b.JPG" ]; then
        rm $b.CR2
    fi
done