Switch database configuration from db.properties to JNDI

JNDI allows the database configuration to be controlled by the Servlet Container so that database parameters are not stored within the war which is replaced each time the application is upgraded.  Also, JNDI gives operations more control over the database configuration than a non-standard properties file.  Default context.xml files still allow the Explorer and REST wars to startup automatically using H2 database config.  Also, the user guide has been updated to reflect the new database configuration.