If you want to save the files outside of the web context (which I agree is the correct way to do this) then you won't be able to directly access them, because they're not in context.
However the problem is easily solved, you provide a file download
servlet which reads the file from the directory, and sends it out as a servlet response.
I would set it up such that
http://myWebSite/myWebApp/getFile/MyFile.txt would download the file.
A servlet mapping in web.xml would map /getFile/* to the file servlet
The servlet would then look at the rest of the url to know which file to send back to the client.
Googling for "file servlet" gives you some good results.