Setting catalina.policy to allow file access by servlets

Question

We have a locally-developed triple store based on b-trees which I want to use for persistent storage in a number of servlet applications. Rather than embed the b-tree index

Answer 1

java.io.FileNotFoundException: 
                /var/data/tdb/kb/node2id.idn (Permission denied)

This is your OS denying access, not Java security. If it was Java security you would get an AccessControlException (or some other form of SecurityException). The user you are running the Tomcat process as presumably does not have access to that file.