Index: lucene/src/java/org/apache/lucene/store/MMapDirectory.java
===================================================================
--- lucene/src/java/org/apache/lucene/store/MMapDirectory.java	(revision 1205157)
+++ lucene/src/java/org/apache/lucene/store/MMapDirectory.java	(working copy)
@@ -26,6 +26,9 @@
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileChannel.MapMode;
 
+import java.util.Map;
+import java.util.WeakHashMap;
+
 import java.security.AccessController;
 import java.security.PrivilegedExceptionAction;
 import java.security.PrivilegedActionException;
@@ -256,6 +259,7 @@
     private ByteBuffer curBuf; // redundant for speed: buffers[curBufIndex]
   
     private boolean isClone = false;
+    private Map<MMapIndexInput,Boolean> clones = new WeakHashMap<MMapIndexInput,Boolean>();
 
     MMapIndexInput(String resourceDescription, RandomAccessFile raf, long offset, long length, int chunkSizePower) throws IOException {
       super(resourceDescription);
@@ -396,9 +400,8 @@
       }
       final MMapIndexInput clone = (MMapIndexInput)super.clone();
       clone.isClone = true;
+      clone.clones = new WeakHashMap<MMapIndexInput,Boolean>();
       clone.buffers = new ByteBuffer[buffers.length];
-      // Since most clones will use only one buffer, duplicate() could also be
-      // done lazy in clones, e.g. when adapting curBuf.
       for (int bufNr = 0; bufNr < buffers.length; bufNr++) {
         clone.buffers[bufNr] = buffers[bufNr].duplicate();
       }
@@ -407,14 +410,31 @@
       } catch(IOException ioe) {
         throw new RuntimeException("Should never happen: " + this, ioe);
       }
+      
+      // register the new clone in our clone list to clean it up on closing:
+      synchronized(this.clones) {
+        this.clones.put(clone, Boolean.TRUE);
+      }
+      
       return clone;
     }
   
     @Override
     public void close() throws IOException {
-      curBuf = null; curBufIndex = 0;
       try {
-        if (isClone || buffers == null) return;
+        curBuf = null; curBufIndex = 0;
+        if (buffers == null) return;
+        
+        // for extra safety close also all clones, so their buffers are unset
+        synchronized(this.clones) {
+          for (final MMapIndexInput clone : this.clones.keySet()) {
+            assert clone.isClone;
+            clone.close(); // should never throw Exception, as clones will not try to unmap
+          }
+          this.clones.clear();
+        }
+        
+        if (isClone) return;
         for (int bufNr = 0; bufNr < buffers.length; bufNr++) {
           // unmap the buffer (if enabled) and at least unset it for GC
           try {
@@ -425,6 +445,7 @@
         }
       } finally {
         buffers = null;
+        clones = null;
       }
     }
   }
Index: lucene/src/test/org/apache/lucene/store/TestMultiMMap.java
===================================================================
--- lucene/src/test/org/apache/lucene/store/TestMultiMMap.java	(revision 1205157)
+++ lucene/src/test/org/apache/lucene/store/TestMultiMMap.java	(working copy)
@@ -18,6 +18,7 @@
  */
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Random;
 
 import org.apache.lucene.analysis.MockAnalyzer;
@@ -47,6 +48,32 @@
     workDir = _TestUtil.getTempDir("TestMultiMMap");
     workDir.mkdirs();
   }
+  
+  public void testCloneSafety() throws Exception {
+    MMapDirectory mmapDir = new MMapDirectory(_TestUtil.getTempDir("testCloneSafety"));
+    IndexOutput io = mmapDir.createOutput("bytes", newIOContext(random));
+    io.writeVInt(5);
+    io.close();
+    IndexInput one = mmapDir.openInput("bytes", IOContext.DEFAULT);
+    IndexInput two = (IndexInput) one.clone();
+    one.close();
+    try {
+      one.readVInt();
+      fail("Must throw IOException or NullPointerException");
+    } catch (IOException ignored1) {
+      // pass
+    } catch (NullPointerException ignored2) {
+      // pass
+    }
+    try {
+      two.readVInt();
+      fail("Must throw IOException or NullPointerException");
+    } catch (IOException ignored1) {
+      // pass
+    } catch (NullPointerException ignored2) {
+      // pass
+    }
+  }
 
   public void testSeekZero() throws Exception {
     for (int i = 0; i < 31; i++) {