I may just not totally understand the problem, but couldn't you just create your uploads folder (in
Java) in a place that has nothing to do with your web-app deployment? /uploads in the root of the current drive, for example or use a system property (like maybe user.dir or user.home) to figure out where the uplaods dir is? Then it wouldn't matter where your app is deployed, it will always reference the uploads dir in the same place.
In my upload app I wrote (
http://www.filenabber.com/filenabber.html) the upload dir is configurable in the web.xml.
Maybe this helps, maybe not.
brian