How to best develop half of a web application?

At work, the task at hand is extending an existing J2EE based product. This means that half of the .war that is to be deployed is hands-off, and the other half is written by us.

The problem I am having is how to get a productive environment. Unfortunately the products file organization is a mess, so there is no way to have a version checked into the version control system as it never would survive an upgrade. Also the deployed app needs to be initialized with a lot of data that is - surprise - saved both in a database and on the filesystem, meaning no easy test db setup.

The developers who have been in the project for a while have used an army of symbolic links to connect the dots, probably inspired by the products overgenerous use of such. But I am not content with what I’ve seen, but I cant really point my finger at what to do. Anyone who has done anything similar?