Setup: Create new course ('Test Course') Navigate to Site administration -> Plugins -> Repositories -> Manage repositories Set "File system" to "Enabled and visible" Press save on the new page shown Once on the "Manage repositories" page scroll to "File system" Click on "Settings" Click on "Create a repository instance" Create new repository called "test1" Create a new file in the repository:  echo Info > ../moodledata/repository/test1/info.txt Test: Navigate to "Test Course" Turn editing on Add file resource Choose a file from file system repository "test1" Select info.txt file Choose "Create an alias/shortcut to the file" option Review mdl_files_reference table and notice new entry there Review mdl_files table and notice new entries Delete the file resource from Moodle course Help Moodle clean up the old entries - age them by 2 weeks: update mdl_files set timemodified = timemodified - (60 * 60 * 24 * 14), timecreated = timecreated - (60 * 60 * 24 * 14); update mdl_files_reference set lastsync = lastsync - (60 * 60 * 24 * 14); Run Moodle cron Review mdl_files table Confirm if the 4 entries have been removed (including draft file entries) If they are still there, run clean-up task manually: php admin/tool/task/cli/schedule_task.php --execute='\core\task\file_trash_cleanup_task' Review the mdl_files_reference table Confirm /info.txt reference entry has been removed