It doesn't look like you've named a graph database bean at all here. I'm not too familiar with the "storeDirectory" attribute, but, here's a sample config I've used with SDN:
<!-- neo4j setup -->
<neo4j:repositories base-package="com.domain.project.repositories"/>
<bean id="graphDatabaseService"
class="org.springframework.data.neo4j.rest.SpringRestGraphDatabase">
<constructor-arg index="0" value="http://hostname:7474/db/data" />
</bean>
<neo4j:config base-package="com.domain.project.entities" graphDatabaseService="graphDatabaseService"/>
The above is for using Neo4j in (remote) server mode via REST, and so you'll likely have to change the graphDatabaseService bean if you're planning on doing this in embedded mode. Something like:
<bean id="graphDbFactory" class="org.neo4j.graphdb.factory.GraphDatabaseFactory"/>
<bean id="graphDatabaseService" scope="singleton" destroy-method="shutdown"
factory-bean="graphDbFactory" factory-method="newEmbeddedDatabase">
<constructor-arg value="target/config-test"/>
</bean>
<neo4j:config graphDatabaseService="graphDatabaseService" base-package="org.example.domain"/>
http://docs.spring.io/spring-data/data-neo4j/docs/3.1.x/reference/html/setup.html is jam-packed with good info on this.
HTH