Yep, all the files have to go through content.php. AFAIK, the only way to get files into /moodledata/repository/ is via FTP so organisations should be able to implement some kind of standardised file structure or best practice for organising their media libraries coherently (one of the problems with Moodle 1.9's file management), which can add up to 10,000's of files very quickly. I'm offering some suggestions here: https://github.com/matbury/SWF-Activity-Module2.5/wiki/Content-Library Other suggestions and ideas would be most welcome
General developer forum
Simple proxy script workaround for Moodle's file API
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