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I'm wondering why WordPress doesn't remove uploads from folder when removed from "Media Library"? I set limit to 5mb on WPMU but even if user removes everything from "Media Library" he can't upload anything new because 5mb limit is still present.

How can I make WPMU remove user uploads when removed from Media Library?

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That's a worst case scenario. Please be confirmed first that, you have deleted files permanently. By default the deleted files are meant to stay in trash.

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Thank you for an answer! Can this be changed? So that when user removes files from "Media Library" the are removed from /uploads/sites/ folder? – Paul Dec 15 '12 at 8:02
I don't think it's a problem making trash first, because you have another option to bypass it by clicking directly on "Delete Permanently". Anyways, have a look at this, whether it's helpful or not. – Mayeenul Islam Dec 15 '12 at 9:01
Maybe I'm blind but there is no "Trash" in Media Library :) You click "delete permanently" and you no longer see this image anywhere but it is still present in /uploads/ folder. I think I'll have to hook into delete_attachment and delete it manually in such event (unless I find a way to do it in Admin Panel). – Paul Dec 15 '12 at 9:27
UPDATE: WP3.5 removes images from Media Library and folder like expected but WP3.5 WPMU doesn't (both when clicked "Delete Permanently"). – Paul Dec 15 '12 at 9:31
UPDATE2: When I did multiple tests now WP3.5 WPMU also removes images from /uploads/ folder (like it should). But I clearly see that it didn't work yesterday for some reason. I still see yesterday's image in /uploads/ folder but it is gone from Media Library. Today it works fine :) – Paul Dec 15 '12 at 9:36

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