Index: oak-store-composite/src/main/java/org/apache/jackrabbit/oak/composite/InitialContentMigrator.java
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
--- oak-store-composite/src/main/java/org/apache/jackrabbit/oak/composite/InitialContentMigrator.java	(revision d76aeb04babb7174016a05e083bbbb6a7636ce81)
+++ oak-store-composite/src/main/java/org/apache/jackrabbit/oak/composite/InitialContentMigrator.java	(date 1537953513000)
@@ -45,6 +45,7 @@
 import java.util.Set;
 
 import static org.apache.jackrabbit.oak.spi.cluster.ClusterRepositoryInfo.CLUSTER_CONFIG_NODE;
+import static org.apache.jackrabbit.oak.spi.namespace.NamespaceConstants.NAMESPACES_PATH;
 
 public class InitialContentMigrator {
 
@@ -52,7 +53,8 @@
 
     private static final String CLUSTER_ID = System.getProperty("oak.composite.seed.clusterId", "1");
 
-    private static final Set<String> DEFAULT_IGNORED_PATHS = ImmutableSet.of("/" + CLUSTER_CONFIG_NODE);
+    private static final Set<String> DEFAULT_IGNORED_PATHS = ImmutableSet
+        .of("/" + CLUSTER_CONFIG_NODE, NAMESPACES_PATH);
 
     private static final Logger LOG = LoggerFactory.getLogger(InitialContentMigrator.class);
 
Index: oak-core/src/main/java/org/apache/jackrabbit/oak/InitialContent.java
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
--- oak-core/src/main/java/org/apache/jackrabbit/oak/InitialContent.java	(revision d76aeb04babb7174016a05e083bbbb6a7636ce81)
+++ oak-core/src/main/java/org/apache/jackrabbit/oak/InitialContent.java	(date 1537952610000)
@@ -83,6 +83,9 @@
             system.child(VersionConstants.JCR_ACTIVITIES)
                     .setProperty(JCR_PRIMARYTYPE, VersionConstants.REP_ACTIVITIES, Type.NAME);
 
+            Namespaces.setupNamespaces(system);
+        } else {
+            NodeBuilder system = builder.getChildNode(JCR_SYSTEM);
             Namespaces.setupNamespaces(system);
         }
 
Index: oak-store-composite/src/test/java/org/apache/jackrabbit/oak/composite/InitialContentMigratorTest.java
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
--- oak-store-composite/src/test/java/org/apache/jackrabbit/oak/composite/InitialContentMigratorTest.java	(revision d76aeb04babb7174016a05e083bbbb6a7636ce81)
+++ oak-store-composite/src/test/java/org/apache/jackrabbit/oak/composite/InitialContentMigratorTest.java	(date 1537953477000)
@@ -16,7 +16,11 @@
  */
 package org.apache.jackrabbit.oak.composite;
 
+import static org.apache.jackrabbit.JcrConstants.JCR_SYSTEM;
 import static org.apache.jackrabbit.oak.spi.cluster.ClusterRepositoryInfo.CLUSTER_CONFIG_NODE;
+import static org.apache.jackrabbit.oak.spi.namespace.NamespaceConstants.NAMESPACES_PATH;
+import static org.apache.jackrabbit.oak.spi.namespace.NamespaceConstants.REP_NAMESPACES;
+import static org.apache.jackrabbit.oak.spi.namespace.NamespaceConstants.REP_NSDATA;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
@@ -29,13 +33,19 @@
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.stream.Collectors;
 
+import org.apache.jackrabbit.oak.InitialContent;
+import org.apache.jackrabbit.oak.OakInitializer;
 import org.apache.jackrabbit.oak.api.CommitFailedException;
 import org.apache.jackrabbit.oak.plugins.document.DocumentMK;
 import org.apache.jackrabbit.oak.plugins.document.DocumentNodeStore;
 import org.apache.jackrabbit.oak.plugins.document.DocumentStore;
 import org.apache.jackrabbit.oak.plugins.document.memory.MemoryDocumentStore;
 import org.apache.jackrabbit.oak.plugins.memory.MemoryNodeStore;
+import org.apache.jackrabbit.oak.plugins.name.NamespaceEditorProvider;
+import org.apache.jackrabbit.oak.plugins.nodetype.TypeEditorProvider;
 import org.apache.jackrabbit.oak.spi.commit.CommitInfo;
+import org.apache.jackrabbit.oak.spi.commit.CompositeEditorProvider;
+import org.apache.jackrabbit.oak.spi.commit.EditorHook;
 import org.apache.jackrabbit.oak.spi.commit.EmptyHook;
 import org.apache.jackrabbit.oak.spi.mount.Mount;
 import org.apache.jackrabbit.oak.spi.mount.MountInfoProvider;
@@ -47,6 +57,35 @@
 
 public class InitialContentMigratorTest {
 
+    @Test
+    public void noMigrationJcrNamespaces() throws Exception {
+        NodeStore seed = new MemoryNodeStore();
+        EditorHook hook = new EditorHook(
+            new CompositeEditorProvider(new NamespaceEditorProvider(), new TypeEditorProvider()));
+        OakInitializer.initialize(seed, new InitialContent(), hook);
+
+        MemoryNodeStore target = new MemoryNodeStore();
+        NodeBuilder targetRootBuilder = target.getRoot().builder();
+        targetRootBuilder.child(JCR_SYSTEM);
+        target.merge(targetRootBuilder, EmptyHook.INSTANCE, CommitInfo.EMPTY);
+
+        MountInfoProvider mip = Mounts.newBuilder().mount("seed", "/first").build();
+
+        // perform migration
+        InitialContentMigrator icm = new InitialContentMigrator(target, seed, mip.getMountByName("seed"));
+        icm.migrate();
+
+        NodeState targetRoot = target.getRoot();
+        assertFalse(NAMESPACES_PATH + "/" + REP_NSDATA + " should not be copied",
+            targetRoot.getChildNode(JCR_SYSTEM).getChildNode(REP_NAMESPACES).hasChildNode(REP_NSDATA));
+        OakInitializer.initialize(target, new InitialContent(), hook);
+
+        targetRoot = target.getRoot();
+        assertTrue(NAMESPACES_PATH + "/" + REP_NSDATA + " should have been created",
+            targetRoot.getChildNode(JCR_SYSTEM).getChildNode(REP_NAMESPACES).hasChildNode(REP_NSDATA));
+
+    }
+
     @Test
     public void migrateContentWithCheckpoints() throws IOException, CommitFailedException {