Hello,
I am in charge on managing many houndreds of moodle (about 500~), i wrot this CLI script in order to automatically update user pics.
* put this file in /admin/cli/updatepics.php
* run it with "--dir=PATH_TO_PICS_FOLDER_HERE"
* it ECHOs out sucsses/failiure.
* based on moodle's batch upload of user pics.
* please VOTE / add some of your own here: http://tracker.moodle.org/browse/MDL-35704
cheers
Omer