Maybe a recursive list of folders under user settings with check boxes to enable/disable access to certain folders. This could also be a great way to enable/disable uploading to certain folders. Seems like this could cause a bit of unnecessary processing every time you opened the setting dialog though. Maybe a link to a popup window that generates the list onload?
Possibly have it output to an .ini file that would be read while populating the list onload EG:
[admin]
c:\folder1 access = 1;
c:\folder1 upload = 1;
c:\folder2 access = 1;
c:\folder2 upload = 0;
then you could populate that user's list box with the allowed folders when uploading
I'd be glad to help, i'm just not very strong in jsp, but i'm decent with javascript
