As pointed in CMS-4239, there are two upload directories: WEB-INF/data/uploads, which is configurable and managed by cocoon, and WEB-INF/data/uploads-users, which isn't configurable and managed by ametys (used in FSUploadManager).
We should use WEB-INF/data/uploads in FSUploadManager (after checking that cocoon accepts that we create folders in its upload directory).
Maybe we should also use a configurable Engine/Scheduler model for the thread.