When you upload files to the bot, they will be analyzed, indexed and stored in the data-directory of the bot. This ensures consistency, fast access and independent metadata as well as some other features like deduplication.
However, this means that you cannot simply upload files via FTP or other means as they would not get indexed and thus not be available for the bot itself. There are plans to allow external files in the future, but there's no focus on that right now.