Index: src/main/java/org/apache/jackrabbit/oak/segment/IllegalSegmentReferences.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/IllegalSegmentReferences.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/IllegalSegmentReferences.java	(working copy)
@@ -37,4 +37,9 @@
         throw new IllegalStateException("invalid use");
     }
 
+    @Override
+    public int size() {
+        throw new IllegalStateException("invalid use");
+    }
+
 }
Index: src/main/java/org/apache/jackrabbit/oak/segment/MutableSegmentReferences.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/MutableSegmentReferences.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/MutableSegmentReferences.java	(working copy)
@@ -85,7 +85,8 @@
      * @return the number of references (segment IDs) accessible from this
      * instance.
      */
-    int size() {
+    @Override
+    public int size() {
         synchronized (lock) {
             return numbers.size();
         }
Index: src/main/java/org/apache/jackrabbit/oak/segment/Segment.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/Segment.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/Segment.java	(working copy)
@@ -229,7 +229,7 @@
         }
 
         int position = HEADER_SIZE + data.position()
-                + getReferencedSegmentIdCount() * SEGMENT_REFERENCE_SIZE;
+                + readReferencedSegmentIdCount() * SEGMENT_REFERENCE_SIZE;
         int maxIndex = data.getInt(position + (recordNumberCount - 1) * 9);
 
         byte[] types = new byte[maxIndex + 1];
@@ -250,10 +250,8 @@
 
     private SegmentReferences readReferencedSegments(
             final SegmentIdProvider idProvider) {
-        checkState(getReferencedSegmentIdCount() + 1 < 0xffff,
-                "Segment cannot have more than 0xffff references");
-
-        final int referencedSegmentIdCount = getReferencedSegmentIdCount();
+        final int referencedSegmentIdCount = readReferencedSegmentIdCount();
+        checkState(referencedSegmentIdCount + 1 < 0xffff, "Segment cannot have more than 0xffff references");
         final int refOffset = data.position() + HEADER_SIZE;
         final SegmentId[] refIds = new SegmentId[referencedSegmentIdCount];
         return new SegmentReferences() {
@@ -276,6 +274,11 @@
                 return id;
             }
 
+            @Override
+            public int size() {
+                return referencedSegmentIdCount;
+            }
+
             @Nonnull
             @Override
             public Iterator<SegmentId> iterator() {
@@ -354,6 +357,10 @@
     }
 
     public int getReferencedSegmentIdCount() {
+        return segmentReferences.size();
+    }
+
+    private int readReferencedSegmentIdCount() {
         return data.getInt(REFERENCED_SEGMENT_ID_COUNT_OFFSET);
     }
 
Index: src/main/java/org/apache/jackrabbit/oak/segment/SegmentBufferWriter.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/SegmentBufferWriter.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/SegmentBufferWriter.java	(working copy)
@@ -38,7 +38,10 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
 import java.util.Set;
+import java.util.UUID;
 
 import javax.annotation.CheckForNull;
 import javax.annotation.Nonnull;
@@ -448,4 +451,16 @@
         return new RecordId(segment.getSegmentId(), recordNumber);
     }
 
+    @Override
+    public Set<UUID> getReferencedSegmentIds() {
+        if (segment == null) {
+            return Collections.emptySet();
+        }
+        Set<UUID> result = new HashSet<>();
+        for (int i = 0; i < segment.getReferencedSegmentIdCount(); i++) {
+            result.add(segment.getReferencedSegmentId(i));
+        }
+        return result;
+    }
+
 }
Index: src/main/java/org/apache/jackrabbit/oak/segment/SegmentBufferWriterPool.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/SegmentBufferWriterPool.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/SegmentBufferWriterPool.java	(working copy)
@@ -27,9 +27,11 @@
 import static java.lang.Thread.currentThread;
 
 import java.io.IOException;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.UUID;
 
 import javax.annotation.Nonnull;
 
@@ -240,4 +242,22 @@
             return wid + "." + writerId;
         }
     }
+
+    @Override
+    public Set<UUID> getReferencedSegmentIds() {
+        Set<UUID> result = new HashSet<>();
+        poolMonitor.enter();
+        try {
+            for (SegmentBufferWriter w : borrowed) {
+                result.addAll(w.getReferencedSegmentIds());
+            }
+            for (SegmentBufferWriter w : disposed) {
+                result.addAll(w.getReferencedSegmentIds());
+            }
+        } finally {
+            poolMonitor.leave();
+        }
+        return result;
+    }
+
 }
Index: src/main/java/org/apache/jackrabbit/oak/segment/SegmentReferences.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/SegmentReferences.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/SegmentReferences.java	(working copy)
@@ -31,4 +31,11 @@
      */
     SegmentId getSegmentId(int reference);
 
+    /**
+     * Return the number of references in this instance.
+     *
+     * @return The numer of segment references in this instance.
+     */
+    int size();
+
 }
Index: src/main/java/org/apache/jackrabbit/oak/segment/SegmentWriter.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/SegmentWriter.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/SegmentWriter.java	(working copy)
@@ -55,6 +55,8 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
 
 import javax.annotation.CheckForNull;
 import javax.annotation.Nonnull;
@@ -1147,4 +1149,8 @@
         this.compactionMonitor = compactionMonitor;
     }
 
+    public Set<UUID> getReferencedSegmentIds() {
+        return writeOperationHandler.getReferencedSegmentIds();
+    }
+
 }
Index: src/main/java/org/apache/jackrabbit/oak/segment/SegmentWriterBuilder.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/SegmentWriterBuilder.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/SegmentWriterBuilder.java	(working copy)
@@ -21,6 +21,9 @@
 
 import static com.google.common.base.Preconditions.checkNotNull;
 
+import java.util.Set;
+import java.util.UUID;
+
 import javax.annotation.Nonnull;
 
 import com.google.common.base.Supplier;
@@ -177,6 +180,12 @@
                     public void flush(@Nonnull SegmentStore store) {
                         throw new UnsupportedOperationException("Cannot write to read-only store");
                     }
+
+                    @Override
+                    public Set<UUID> getReferencedSegmentIds() {
+                        throw new UnsupportedOperationException("Cannot write to read-only store");
+                    }
+
                 });
     }
 
Index: src/main/java/org/apache/jackrabbit/oak/segment/WriteOperationHandler.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/WriteOperationHandler.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/WriteOperationHandler.java	(working copy)
@@ -20,6 +20,8 @@
 package org.apache.jackrabbit.oak.segment;
 
 import java.io.IOException;
+import java.util.Set;
+import java.util.UUID;
 
 import javax.annotation.Nonnull;
 
@@ -62,4 +64,14 @@
      * @throws IOException
      */
     void flush(@Nonnull SegmentStore store) throws IOException;
+
+    /**
+     * Returns the identifiers of segments referenced by the data written by
+     * this instance.
+     *
+     * @return The identifiers of segments referenced by the data written by
+     * this instance.
+     */
+    Set<UUID> getReferencedSegmentIds();
+
 }
Index: src/main/java/org/apache/jackrabbit/oak/segment/file/FileStore.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/segment/file/FileStore.java	(revision 1790395)
+++ src/main/java/org/apache/jackrabbit/oak/segment/file/FileStore.java	(working copy)
@@ -816,6 +816,11 @@
                     bulkRefs.add(id.asUUID());
                 }
             }
+            for (UUID id : segmentWriter.getReferencedSegmentIds()) {
+                if (!SegmentId.isDataSegmentId(id.getLeastSignificantBits())) {
+                    bulkRefs.add(id);
+                }
+            }
             CleanupResult cleanupResult = tarFiles.cleanup(bulkRefs, compactionResult.reclaimer());
             if (cleanupResult.isInterrupted()) {
                 gcListener.info("TarMK GC #{}: cleanup interrupted", GC_COUNT);