Best Practices for comparing versions of an application?

System

I'm working on the design of a Content-Provisioning-like solution (using TeamSite and OpenDeploy) and am stuck on the following:

I'd like to get an exploded archive (.war) into a workarea and then be able to do a TeamSite compare (against staging or an edition) to find the differences between the versions of the app.

Is there a process any of you follow (or would suggest) to enable what I'm looking for? With the initial testing I've done, I always end up with all files in the workarea appearing as modified - which invalidates the compare function.

This is TeamSite 6.1 on Solaris.

Thanks!
Wally