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What are the best practices to clean up the uploads folder of orphaned files?

Question asked by Daniela Scheiwe on Mar 7, 2014
Latest reply on Jun 2, 2015 by sonesay inthavong
I was trying to cleanup the upload-folder using "Remove missed files from upload directory" in the repair menu. The process ran for more than one hour and it also moved a bunch of files to the "deleted"-directory (only ~50MB of more than 2GB).

I have looked up several of the remaining file names (IDs) in the database and found some, mostly PDF attachments, but most of the files in the upload folder were not existing in the database. So I guess they don't have any relations to any records and could be deleted. 
So I wonder: Why weren't they deleted, and how can I find out which files are safe to delete?