I have just committed a new version with various changes, including support for structured proofs with a new version of Vampire. Please download a new Vampire binary from http://www.cl.cam.ac.uk/research/ hvg/Isabelle/atp-linkup.html (Linux only) if you use Vampire.
The environment variables E_HOME, SPASS_HOME and VAMPIRE_HOME are now set automatically in the main settings file. Simplest is if you put symblinks to eproof, SPASS and vampire in your $ISABELLE_HOME/contrib directory. Structured proofs are not working at the moment due to a type inference problem. However, apply-proofs should always appear. I hope this can be fixed soon. There's also a problem that text from the PG output is no longer selectable. I'm afraid I have no idea what's going on there. Larry