Using the database files directly locks them preventing any other code from being able to access the DB. This is the correct approach for the Neo4J Server plugin, however for the GeoServer plugin, this prevents being able to run either the Neo4J Server exposing the bolt protocol or any other consumer using an embedded database due to the store being locked. It would improve the integration experience if the GeoServer plugin used the Neo4J Java Driver instead as this is network based and does not prevent the Neo server running on the same files: https://neo4j.com/developer/java/