start safe_mysqld like this to catch slow queries:
./bin/safe_mysqld --log-slow-queries &
OR
To use it, you need to add --log-slow-queries to your mysqld startup.
I added it to my /etc/rc.d/init.d/mysql file like so:
$bindir/safe_mysqld --user=$mysql_daemon_user --datadir=$datadir --pid-file=$pid_file --log=$log_file --log-slow-queries &
It does appear to put stuff into a different place, namely:
/var/lib/mysql/hostname-slow.log
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