goto implimenation (ctrl-alt-B) problems

I love IDEA 3 and I am trying to move to 4.5.

The project tree that I am working with probably sucks but I cannot change it and IDEA 3 works just fine with it so I assume that I should be able to configure 4.5 to work with it as well.

The project that get's converted by 4.5 does not seem to allow to me to navigate between interfaces and classes and so forth.

If possible I would like some assistance in setting up my new project.

Not sure what info to include but,
the project uses a webapp and ejb.
Xdoclet gerates all of our EJB interfaces and ejb-jar.xml.

Once the intitial build is performed I have all of the pieces needed, but they are not in a module form.
I have included the important pieces:

ar/
deploy/
ar.ear/
ar.jar/
META-INF/
ejb-jar.xml
ar.sar
ar.war/
WEB-INF/
classes
jsp-files
web.xml
lib
src/
com/
ejb
web/
action
form

Our JBoss dev server will point to the deploy directory.
I do not need IDEA to build,deploy or run my app. I just want the full navigation and refactoring that I enjoy with IDEA 3.

Hope someone can help.

Thanks

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