The file manipulation features of Universal Email will allow you to upload and delete files. This in combination with recording the files values and details in a db table with DataAssist could help you achieve most of these goals. You can upload more than one file at a time on a page but you will need individual file fields for each upload. Allowing the users control over creating directories is not a feature of these tools.
To build this out you would probably want to use DA to create all the pages for managing the data and get all that worked out first, then you can go into these pages and add in upload and delete file functionality where you need it.