Not a dev myself, but do admin several instances of Moodle on Linux platform. Moodle config (automated backups or single course backups) are not done all at once ... but rather one at a time. Backups are intensive processing.
So think to get what you want you'll have to resort to the scripts in moodlecode/admin/cli/ .... of which there is one for backing up a single course - backup.php
One could create a txt file that is nothing more than the course ID's you desire to backup and then loop a bash shell script through the cids.txt file to backup each course. I'd also make sure to use the 'destination' option of backup.php so that the backups don't get lost in the sea of files in moodledata/filedir/
Here's an example of a bash shell script that backs up just one course:
echo 'This backups up the course ID given it from list above.';
echo 'Course ID: '$1;
echo 'paused ...';
php backup.php --courseid=$1 --destination=/home/backup/m33/
A cli script to get course ID's:
mysql -u root -p'' -e "use moodle2;select id from mdl_course;" > courseids.txt;cat courseids.txt
You'd have to edit the courseids.txt file and remove the first line so that all that file contains is the CID's you want to backup.
Here's a looper bash shell script example:
for i in `cat ./courselist2.txt`
echo "Course ID in que:" $i;
php backup.php --courseid=$i --destination=/home/clibackups/
The courselist2.txt file is nothing more than a text file with the course ID's to backup ... each CID on a single line:
I'd skip CID 1 as that is the front page ... which cannot be restored to the front page anyway.
'spirit of sharing', Ken