This code does not work
Session session = RepositoryReferenceFactory.getRepository("test-file").login();
ValueFactory vf = session.getValueFactory();

Node root = session.getRootNode();
Node file = root.addNode("createfile.mode", "nt:file");
Node content = file.addNode("jcr:content", "nt:resource");
content.setProperty("jcr:data", vf.createBinary(new ByteArrayInputStream("Write 1".getBytes())));
session.save();

session.getNode("/createfile.mode");

It throws an exception
javax.jcr.PathNotFoundException: Unable to find "{}createfile.mode"; lowest existing path is "/"
at org.modeshape.jcr.JcrSession.getNode(JcrSession.java:779)
at org.modeshape.jcr.JcrSession.getNode(JcrSession.java:649)
at org.modeshape.jcr.JcrSession.getNode(JcrSession.java:106)
at org.jboss.soa.modeshape.qa.tests.BrokenFileConnectorTest.fileCreate(BrokenFileConnectorTest.java:31)

Connector configuration
<mode:source jcr:name="test-file"
mode:classname="org.modeshape.connector.filesystem.FileSystemSource"
mode:creatingWorkspaceAllowed="true"
mode:retryLimit="3"
mode:defaultWorkspaceName="default"
mode:filenameFilter="*.mode"
mode:updatesAllowed="true"
>
<xsl:attribute name="mode:workspaceRootPath">
<xsl:value-of select="$repositorypath"/>
</xsl:attribute>
<mode:predefinedWorkspaceNames>file1</mode:predefinedWorkspaceNames>
<mode:predefinedWorkspaceNames>file2</mode:predefinedWorkspaceNames>
<mode:predefinedWorkspaceNames>custom-federated</mode:predefinedWorkspaceNames>
</mode:source>

The file is not physically created after the session.save(). Creating folders works reliably.
This code was worked in ER2.