- First thing to check when packaging applications. Is it possible to move the file location. By the use of the apps. registry settings (check regmon, look if the app reads possible file locations). Also check ini files for file locations.
- U can't influence the location? Then u could give some special rights to the users group account on the file system. Check the advanced options of security. Remember u can set rights for "This folder, subfolder and files" , but you could also grant rights only for files etc. This is very handy in this sort of situations. If this is a solution for u, use the open source tool SetACL (also has a gui --> EasyACL) to implement your solution.
Granting priviliges is very normal in packaging for locked down environments. Otherwise my job would get a lot harder.... probably impossible.
Hope this helps u out a bit. If not maybe I know the app. Let me know.
Greetz