The file system connector only works with "nt:file" and "nt:resource" nodes, as described in https://docs.jboss.org/author/display/MODE/Storing+files+and+folders. Also, see all the configuration options for the connector: https://docs.jboss.org/author/display/MODE/File+system+connector.
Just to be clear, the connector allows nodes and properties to be stored directly on the file system. It is not the same thing as a binary store, which the repository uses to store binary values.
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We now have a Wildfly/EAP test which verifies that files are stored correctly on disk as long as you're working with nt:file, nt:folder and nt:resource types: modeshape/FederationIntegrationTest.java at master · ModeShape/modeshape · GitHub