Java on linux question

Our company is currently migrating our technology from NT/Novell to Linux.
Recently, a developer approached me with a java on linux question that I
could not answer. He was writing a java app that will run in a JVM on linux
and access the linux file system using java IO. Now we dont want anything
like that running as root so what is the best way for java io to interact
with user/group permissions on the file system? Apperently when this app was
on novell he was able to use a novell user class. Thanks for reading my
post.

- Joel Dudley