I fixed the problem in EntryVisitor.java by testing for the File being a directory first. The code in method searchDir() now looks like this:

        for (int i = 0; i < files.length; i++) {
            File file = files[i];
            if (file.isDirectory()) {
                // It's a directory , so call ourselves recursively
                this.searchDir(file);
            } else if (isJar(file)) {
                // It's a jar
                this.searchJar(file);
            } else {
                // If it's any other sort of file, visit it anyway
                visit(file);
            }
        }

However, have a look at the code in this post JNDI problems with Tomcat. If you look at the second code block you can see some code that loads a class and then tries to find where it was loaded from by getting the source code for the class and then the location for that. This definitely works with Tomcat (as long as the classes have been compiled with enough debugging information which is normally the case).