On a Mac I had a couple of problems: the quotes have been changed in the HTML to opening and closing quotes, which are different characters that bash doesn\’t recognize. Second, I needed to add \"\" around \"$db\" due to the spaces in the filename on a Mac. The final version that did the job is:

#!/bin/bash
db=\"/Users/rcusack/Library/Application Support/Mendeley Desktop/rhodricusack@gmail.com@www.mendeley.com.sqlite\" # set the db-file here. The location depends on the OS you use.
limit=\"WHERE confirmed=\’true\’ AND type=\’JournalArticle\’\"
sqlite3 \"$db\" \"SELECT id FROM Documents $limit\" > temp_ids.txt
cat temp_ids.txt | while read line
do
long=$(sqlite3 \"$db\" \"SELECT publication FROM Documents WHERE id=$line\")
echo \"long = $long\"
echo \"The id is $line\"
line_pubm=$(grep -i -n -m 1 \"$long\" J_Medline.txt | cut -f1 -d:)
echo \"linenumber in pubm= $line_pubm\"
abbr_linen=$(( $line_pubm + 1 ))
short=$(sed -n ${abbr_linen}p J_Medline.txt | sed \’s/MedAbbr: //\’ | tr -cd \’[:alnum:]\’)
echo “short= $short”
LEN=$(echo ${#short})
echo $LEN
if [ \"$short\" ]; then
echo $short
echo $line
sqlite3 \"$db\" \"UPDATE Documents SET publication=\’${short}\’ WHERE id=${line}\"
# sqlite3 $db
# make a security update of your sqlite-file and replace the echo from above with sqlite3 $db
else
echo \"no or short shortname (<3 chars) - not changed\"
fi
done

MendeleyScript.sh: 2: Ltd./Mendeley: not found

However, when I paste the location from your description, i pop right into the Mendeley folder. What am I doing wrong?