I'm not sure what you mean. We already have the media folder where images/css/js belongs that's installed with extensions. This separation of PHP code and those assets that are send to the browser allows us to eventually move the PHP code outside the web root and/or the assets to a different domain or even a CDN
For media that is uploaded by the user there is the images folder. However there could reasonably be more. The biggest issue we have there is the lack of metadata and ACL. Right now the image manager is just a simple representation of the files on disk.
Best regards
Rouven
The short answer is hat they should go into the /media folder.
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