Index: src/test/org/apache/lucene/index/TestPerSegmentDeletes.java
===================================================================
--- src/test/org/apache/lucene/index/TestPerSegmentDeletes.java	(revision 0)
+++ src/test/org/apache/lucene/index/TestPerSegmentDeletes.java	(revision 0)
@@ -0,0 +1,269 @@
+package org.apache.lucene.index;
+
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.lucene.analysis.MockAnalyzer;
+import org.apache.lucene.document.Document;
+import org.apache.lucene.index.DocumentsWriter.SegmentDeletes;
+import org.apache.lucene.index.TermsEnum.SeekStatus;
+import org.apache.lucene.store.Directory;
+import org.apache.lucene.store.MockDirectoryWrapper;
+import org.apache.lucene.store.RAMDirectory;
+import org.apache.lucene.util.ArrayUtil;
+import org.apache.lucene.util.Bits;
+import org.apache.lucene.util.BytesRef;
+import org.apache.lucene.util.LuceneTestCase;
+import org.apache.lucene.util.Version;
+
+public class TestPerSegmentDeletes extends LuceneTestCase {
+  public void testDeletes1() throws Exception {
+    IndexWriter.debug2 = System.out;
+    Directory dir = new MockDirectoryWrapper(new RAMDirectory());
+    IndexWriterConfig iwc = new IndexWriterConfig(Version.LUCENE_CURRENT,
+        new MockAnalyzer());
+    iwc.setMergeScheduler(new SerialMergeScheduler());
+    iwc.setMaxBufferedDocs(5000);
+    iwc.setRAMBufferSizeMB(400);
+    RangeMergePolicy fsmp = new RangeMergePolicy(false);
+    iwc.setMergePolicy(fsmp);
+    IndexWriter writer = new IndexWriter(dir, iwc);
+    Document doc = new Document();
+    for (int x = 0; x < 5; x++) {
+      writer.addDocument(TestIndexWriterReader.createDocument(x, "1", 2));
+      System.out.println("numRamDocs(" + x + ")" + writer.numRamDocs());
+    }
+    System.out.println("commit1");
+    writer.commit();
+    //assertEquals(1, writer.docWriter.lastSegmentIndex);
+    assertEquals(1, writer.segmentInfos.size());
+    for (int x = 5; x < 10; x++) {
+      writer.addDocument(TestIndexWriterReader.createDocument(x, "2", 2));
+      System.out.println("numRamDocs(" + x + ")" + writer.numRamDocs());
+    }
+    System.out.println("commit2");
+    writer.commit();
+    //assertEquals(2, writer.docWriter.lastSegmentIndex);
+    assertEquals(2, writer.segmentInfos.size());
+    
+    for (int x = 10; x < 15; x++) {
+      writer.addDocument(TestIndexWriterReader.createDocument(x, "3", 2));
+      System.out.println("numRamDocs(" + x + ")" + writer.numRamDocs());
+    }
+    System.out.println("flush(false, false, false)");
+    writer.flush(false, false, false);
+    //assertEquals(2, writer.docWriter.lastSegmentIndex);
+    assertEquals(3, writer.segmentInfos.size());
+    
+    // added docs are in the ram buffer
+    for (int x = 15; x < 20; x++) {
+      writer.addDocument(TestIndexWriterReader.createDocument(x, "4", 2));
+      System.out.println("numRamDocs(" + x + ")" + writer.numRamDocs());
+    }
+    assertTrue(writer.numRamDocs() > 0);
+    // delete from the ram buffer
+    writer.deleteDocuments(new Term("id", Integer.toString(13)));
+    
+    Term id3 = new Term("id", Integer.toString(3));
+    
+    // delete from the 1st segment
+    writer.deleteDocuments(id3);
+    
+    assertTrue(writer.numRamDocs() > 0);
+    
+    System.out
+        .println("segdels1:" + writer.docWriter.deletesToString());
+    
+    assertTrue(writer.docWriter.segmentDeletes.size() > 0);
+    
+    // we cause a merge to happen
+    fsmp.doMerge = true;
+    fsmp.start = 0;
+    fsmp.length = 2;
+    System.out.println("maybeMerge "+writer.segmentInfos);
+    
+    SegmentInfo info0 = writer.segmentInfos.get(0);
+    SegmentInfo info1 = writer.segmentInfos.get(1);
+    
+    writer.maybeMerge();
+    System.out.println("maybeMerge after "+writer.segmentInfos);
+    // there should be docs in RAM
+    assertTrue(writer.numRamDocs() > 0);
+    
+    // assert we've merged the 1 and 2 segments
+    // and still have a segment leftover == 2
+    assertEquals(2, writer.segmentInfos.size());
+    assertFalse(segThere(info0, writer.segmentInfos));
+    assertFalse(segThere(info1, writer.segmentInfos));
+    
+    System.out.println("segdels2:" + writer.docWriter.deletesToString());
+    
+    assertTrue(writer.docWriter.segmentDeletes.size() > 0);
+    
+    IndexReader r = writer.getReader();
+    IndexReader r1 = r.getSequentialSubReaders()[0];
+    printDelDocs(r1.getDeletedDocs());
+    int[] docs = toDocsArray(id3, null, r);
+    System.out.println("id3 docs:"+Arrays.toString(docs));
+    // there shouldn't be any docs for id:3
+    assertTrue(docs == null);
+    r.close();
+    
+    part2(writer, fsmp);
+    
+    // System.out.println("segdels2:"+writer.docWriter.segmentDeletes.toString());
+    System.out.println("close");
+    writer.close();
+    dir.close();
+  }
+  
+  void part2(IndexWriter writer, RangeMergePolicy fsmp) throws Exception {
+    for (int x = 20; x < 25; x++) {
+      writer.addDocument(TestIndexWriterReader.createDocument(x, "5", 2));
+      System.out.println("numRamDocs(" + x + ")" + writer.numRamDocs());
+    }
+    writer.flush(false, true, false);
+    for (int x = 25; x < 30; x++) {
+      writer.addDocument(TestIndexWriterReader.createDocument(x, "5", 2));
+      System.out.println("numRamDocs(" + x + ")" + writer.numRamDocs());
+    }
+    writer.flush(false, true, false);
+    
+    System.out.println("infos3:"+writer.segmentInfos);
+    
+    Term delterm = new Term("id", "8");
+    writer.deleteDocuments(delterm);
+    System.out.println("segdels3:" + writer.docWriter.deletesToString());
+    
+    fsmp.doMerge = true;
+    fsmp.start = 1;
+    fsmp.length = 2;
+    writer.maybeMerge();
+    
+    // deletes for info1, the newly created segment from the 
+    // merge should have no deletes because they were applied in
+    // the merge
+    SegmentInfo info1 = writer.segmentInfos.get(1);
+    assertFalse(exists(info1, writer.docWriter.segmentDeletes));
+    
+    System.out.println("infos4:"+writer.segmentInfos);
+    System.out.println("segdels4:" + writer.docWriter.deletesToString());
+  }
+  
+  static boolean exists(SegmentInfo info, Map<SegmentInfo,SegmentDeletes> map) {
+    if (!map.containsKey(info)) return false;
+    SegmentDeletes dels = map.get(info);
+    return dels.any();
+  }
+  
+  boolean segThere(SegmentInfo info, SegmentInfos infos) {
+    for (SegmentInfo si : infos) {
+      if (si.name.equals(info.name)) return true; 
+    }
+    return false;
+  }
+  
+  public static void printDelDocs(Bits bits) {
+    if (bits == null) return;
+    for (int x = 0; x < bits.length(); x++) {
+      System.out.println(x + ":" + bits.get(x));
+    }
+  }
+  
+  public static int[] toDocsArray(Term term, Bits bits, IndexReader reader)
+      throws IOException {
+    Fields fields = MultiFields.getFields(reader);
+    Terms cterms = fields.terms(term.field);
+    TermsEnum ctermsEnum = cterms.iterator();
+    SeekStatus ss = ctermsEnum.seek(new BytesRef(term.text()), false);
+    if (ss.equals(SeekStatus.FOUND)) {
+      DocsEnum docsEnum = ctermsEnum.docs(bits, null);
+      return toArray(docsEnum);
+    }
+    return null;
+  }
+  
+  public static int[] toArray(DocsEnum docsEnum) throws IOException {
+    List<Integer> docs = new ArrayList<Integer>();
+    while (docsEnum.nextDoc() != DocsEnum.NO_MORE_DOCS) {
+      int docID = docsEnum.docID();
+      docs.add(docID);
+    }
+    return ArrayUtil.toIntArray(docs);
+  }
+  
+  public class RangeMergePolicy extends MergePolicy {
+    boolean doMerge = false;
+    int start;
+    int length;
+    
+    private final boolean useCompoundFile;
+    
+    private RangeMergePolicy(boolean useCompoundFile) {
+      this.useCompoundFile = useCompoundFile;
+    }
+    
+    @Override
+    public void close() {}
+    
+    public MergeSpecification findMerges(SegmentInfos segmentInfos)
+        throws CorruptIndexException, IOException {
+      MergeSpecification ms = new MergeSpecification();
+      if (doMerge) {
+        SegmentInfos mergeInfos = new SegmentInfos();
+        for (int x=start; x < (start+length); x++) {
+          mergeInfos.add(segmentInfos.get(x));
+        }
+        OneMerge om = new OneMerge(mergeInfos, false);
+        ms.add(om);
+        doMerge = false;
+        return ms;
+      }
+      return null;
+    }
+    
+    @Override
+    public MergeSpecification findMergesForOptimize(SegmentInfos segmentInfos,
+        int maxSegmentCount, Set<SegmentInfo> segmentsToOptimize)
+        throws CorruptIndexException, IOException {
+      return null;
+    }
+    
+    @Override
+    public MergeSpecification findMergesToExpungeDeletes(
+        SegmentInfos segmentInfos) throws CorruptIndexException, IOException {
+      return null;
+    }
+    
+    @Override
+    public boolean useCompoundDocStore(SegmentInfos segments) {
+      return useCompoundFile;
+    }
+    
+    @Override
+    public boolean useCompoundFile(SegmentInfos segments, SegmentInfo newSegment) {
+      return useCompoundFile;
+    }
+  }
+}
Index: src/java/org/apache/lucene/index/BufferedDeletes.java
===================================================================
--- src/java/org/apache/lucene/index/BufferedDeletes.java	(revision 1030113)
+++ src/java/org/apache/lucene/index/BufferedDeletes.java	(working copy)
@@ -49,6 +49,13 @@
       terms = new HashMap<Term,Num>();
     }
   }
+  
+  @Override
+  public String toString() {
+    return "BufferedDeletes [numTerms=" + numTerms + ", terms=" + terms
+        + ", queries=" + queries + ", docIDs=" + docIDs + ", bytesUsed="
+        + bytesUsed + ", doTermSort=" + doTermSort + "]";
+  }
 
   // Number of documents a delete term applies to.
   final static class Num {
Index: src/java/org/apache/lucene/index/MergePolicy.java
===================================================================
--- src/java/org/apache/lucene/index/MergePolicy.java	(revision 1030113)
+++ src/java/org/apache/lucene/index/MergePolicy.java	(working copy)
@@ -17,15 +17,17 @@
  * limitations under the License.
  */
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.lucene.index.DocumentsWriter.SegmentDeletes;
+import org.apache.lucene.index.MergePolicy.MergeSpecification;
 import org.apache.lucene.store.Directory;
 import org.apache.lucene.util.SetOnce;
 import org.apache.lucene.util.SetOnce.AlreadySetException;
 
-import java.io.IOException;
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Set;
-
 /**
  * <p>Expert: a MergePolicy determines the sequence of
  * primitive merge operations to be used for overall merge
Index: src/java/org/apache/lucene/index/DocumentsWriter.java
===================================================================
--- src/java/org/apache/lucene/index/DocumentsWriter.java	(revision 1030113)
+++ src/java/org/apache/lucene/index/DocumentsWriter.java	(working copy)
@@ -17,18 +17,22 @@
  * limitations under the License.
  */
 
+import static org.apache.lucene.util.ByteBlockPool.BYTE_BLOCK_MASK;
+import static org.apache.lucene.util.ByteBlockPool.BYTE_BLOCK_SIZE;
+
 import java.io.IOException;
 import java.io.PrintStream;
 import java.text.NumberFormat;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
-import java.util.Map;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Map.Entry;
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicLong;
-import java.util.concurrent.locks.ReentrantLock;
 
 import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.document.Document;
@@ -43,11 +47,9 @@
 import org.apache.lucene.store.RAMFile;
 import org.apache.lucene.util.ArrayUtil;
 import org.apache.lucene.util.Constants;
+import org.apache.lucene.util.RamUsageEstimator;
 import org.apache.lucene.util.RecyclingByteBlockAllocator;
 import org.apache.lucene.util.ThreadInterruptedException;
-import org.apache.lucene.util.RamUsageEstimator;
-import static org.apache.lucene.util.ByteBlockPool.BYTE_BLOCK_MASK;
-import static org.apache.lucene.util.ByteBlockPool.BYTE_BLOCK_SIZE;
 
 /**
  * This class accepts multiple added documents and directly
@@ -152,7 +154,101 @@
   private final int maxThreadStates;
 
   List<String> newFiles;
+  Map<SegmentInfo,SegmentDeletes> segmentDeletes = new HashMap<SegmentInfo,SegmentDeletes>();
+  int lastSegmentIndex = 0;
+  SegmentInfo lastSegment;
+  final AtomicLong segmentDeletesBytesUsed = new AtomicLong(0);
+  private static Term[] EMPTY_TERM_ARRAY = new Term[0];
+  
+  public String deletesToString() {
+    return "lastSegmentIndex:"+lastSegmentIndex+" segmentDeletes:"+segmentDeletes+" deletesInRAM:"+deletesInRAM+" deletesFlushed:"+deletesFlushed;
+  }
+  
+  // if the index is less than or equals to the last segment index
+  // return the deletes of the last segment
+  synchronized SegmentDeletes getSegmentDeletes(int index, SegmentInfos allInfos) {
+    assert index >= 0;
+    
+    SegmentInfo info = null;
+    if (index <= lastSegmentIndex) {
+      info = allInfos.get(lastSegmentIndex);
+    } else {
+      info = allInfos.get(index);
+    }
+    return segmentDeletes.get(info);
+  }
+  
+  static class SegmentDeletes {
+    private Set<Term> terms = new HashSet<Term>();
+	  private Set<Query> queries = new HashSet<Query>();
+	  SegmentInfo info;
+	  long bytesUsed = 0;
+	  
+	  public SegmentDeletes(SegmentInfo info) {
+	    this.info = info;
+	  }
+	  
+	  void merge(SegmentDeletes mergeDels) {
+	    assert mergeDels.info.equals(info);
+	    addTerms(mergeDels.terms);
+	    addQueries(mergeDels.queries);
+	  }
+	  
+	  void addTerm(Term term) {
+	    if (terms.add(term)) {
+	      // we're only adding the term pointer, not the actual 
+	      // term bytes because those have been added for
+	      // deletes flushed
+	      bytesUsed += BYTES_PER_DEL_TERM;
+	    }
+	  }
+	  
+	  void addTerms(Collection<Term> ts) {
+	    for (Term t : ts) {
+	      addTerm(t);
+	    }
+	  }
+	  
+	  void addQueries(Collection<Query> qs) {
+      for (Query q : qs) {
+        addQuery(q);
+      }
+    }
+	  
+	  void addQuery(Query query) {
+      if (queries.add(query)) {
+        bytesUsed += BYTES_PER_DEL_QUERY;
+      }
+    }
+	  
+	  public void clear(DocumentsWriter dw) {
+	    // remove the bytes used by this deletes object
+	    for (int x=0; x < terms.size(); x++) {
+	      dw.segmentDeletesBytesUsed.addAndGet(-BYTES_PER_DEL_TERM);
+	    }
+	    for (int x=0; x < queries.size(); x++) {
+        dw.segmentDeletesBytesUsed.addAndGet(-BYTES_PER_DEL_QUERY);
+      }
+	    terms.clear();
+	    queries.clear();
+	  }
+	  
+	  public Term[] getSortedTerms() {
+	    Term[] arr = terms.toArray(EMPTY_TERM_ARRAY);
+	    Arrays.sort(arr);
+	    return arr;
+	  }
+	  
+	  @Override
+    public String toString() {
+      return "Deletes [terms=" + terms + ", queries=" + queries + "]";
+    }
 
+	  boolean any() {
+      return terms.size() > 0 || queries.size() > 0;
+	  }
+  }
+  
   static class DocState {
     DocumentsWriter docWriter;
     Analyzer analyzer;
@@ -329,6 +425,9 @@
     if (consumer instanceof DocFieldProcessor) {
       docFieldProcessor = (DocFieldProcessor) consumer;
     }
+    if (writer.segmentInfos.size() > 0) {
+      lastSegmentIndex = writer.segmentInfos.size() - 1;
+    }
   }
 
   /** Returns true if any of the fields in the current
@@ -735,7 +834,7 @@
    * flush is pending.  If delTerm is non-null then we
    * buffer this deleted term after the thread state has
    * been acquired. */
-  synchronized DocumentsWriterThreadState getThreadState(Document doc, Term delTerm) throws IOException {
+  synchronized DocumentsWriterThreadState getThreadState(Document doc, Term delTerm, SegmentInfos infos) throws IOException {
 
     final Thread currentThread = Thread.currentThread();
 
@@ -785,7 +884,7 @@
       assert writer.testPoint("DocumentsWriter.ThreadState.init start");
 
       if (delTerm != null) {
-        addDeleteTerm(delTerm, state.docState.docID);
+        addDeleteTerm(delTerm, state.docState.docID, infos);
         state.doFlushAfter = timeToFlushDeletes();
       }
 
@@ -822,21 +921,21 @@
 
   /** Returns true if the caller (IndexWriter) should now
    * flush. */
-  boolean addDocument(Document doc, Analyzer analyzer)
+  boolean addDocument(Document doc, Analyzer analyzer, SegmentInfos infos)
     throws CorruptIndexException, IOException {
-    return updateDocument(doc, analyzer, null);
+    return updateDocument(doc, analyzer, null, infos);
   }
 
-  boolean updateDocument(Term t, Document doc, Analyzer analyzer)
+  boolean updateDocument(Term t, Document doc, Analyzer analyzer, SegmentInfos infos)
     throws CorruptIndexException, IOException {
-    return updateDocument(doc, analyzer, t);
+    return updateDocument(doc, analyzer, t, infos);
   }
 
-  boolean updateDocument(Document doc, Analyzer analyzer, Term delTerm)
+  boolean updateDocument(Document doc, Analyzer analyzer, Term delTerm, SegmentInfos infos)
     throws CorruptIndexException, IOException {
     
     // This call is synchronized but fast
-    final DocumentsWriterThreadState state = getThreadState(doc, delTerm);
+    final DocumentsWriterThreadState state = getThreadState(doc, delTerm, infos);
 
     final DocState docState = state.docState;
     docState.doc = doc;
@@ -939,43 +1038,43 @@
       throw new AlreadyClosedException("this IndexWriter is closed");
   }
 
-  boolean bufferDeleteTerms(Term[] terms) throws IOException {
+  boolean bufferDeleteTerms(Term[] terms, SegmentInfos infos) throws IOException {
     synchronized(this) {
       waitReady(null);
       for (int i = 0; i < terms.length; i++)
-        addDeleteTerm(terms[i], numDocsInRAM);
+        addDeleteTerm(terms[i], numDocsInRAM, infos);
     }
     return timeToFlushDeletes();
   }
 
-  boolean bufferDeleteTerm(Term term) throws IOException {
+  boolean bufferDeleteTerm(Term term, SegmentInfos infos) throws IOException {
     synchronized(this) {
       waitReady(null);
-      addDeleteTerm(term, numDocsInRAM);
+      addDeleteTerm(term, numDocsInRAM, infos);
     }
     return timeToFlushDeletes();
   }
 
-  boolean bufferDeleteQueries(Query[] queries) throws IOException {
+  boolean bufferDeleteQueries(Query[] queries, SegmentInfos infos) throws IOException {
     synchronized(this) {
       waitReady(null);
       for (int i = 0; i < queries.length; i++)
-        addDeleteQuery(queries[i], numDocsInRAM);
+        addDeleteQuery(queries[i], numDocsInRAM, infos);
     }
     return timeToFlushDeletes();
   }
 
-  boolean bufferDeleteQuery(Query query) throws IOException {
+  boolean bufferDeleteQuery(Query query, SegmentInfos infos) throws IOException {
     synchronized(this) {
       waitReady(null);
-      addDeleteQuery(query, numDocsInRAM);
+      addDeleteQuery(query, numDocsInRAM, infos);
     }
     return timeToFlushDeletes();
   }
 
   synchronized boolean deletesFull() {
     return (ramBufferSize != IndexWriterConfig.DISABLE_AUTO_FLUSH &&
-            (deletesInRAM.bytesUsed + deletesFlushed.bytesUsed + bytesUsed()) >= ramBufferSize) ||
+            (segmentDeletesBytesUsed.get()+deletesInRAM.bytesUsed + deletesFlushed.bytesUsed + bytesUsed()) >= ramBufferSize) ||
       (maxBufferedDeleteTerms != IndexWriterConfig.DISABLE_AUTO_FLUSH &&
        ((deletesInRAM.size() + deletesFlushed.size()) >= maxBufferedDeleteTerms));
   }
@@ -990,7 +1089,7 @@
     // when merges (which always apply deletes) are
     // infrequent.
     return (ramBufferSize != IndexWriterConfig.DISABLE_AUTO_FLUSH &&
-            (deletesInRAM.bytesUsed + deletesFlushed.bytesUsed) >= ramBufferSize/2) ||
+            (segmentDeletesBytesUsed.get()+deletesInRAM.bytesUsed + deletesFlushed.bytesUsed) >= ramBufferSize/2) ||
       (maxBufferedDeleteTerms != IndexWriterConfig.DISABLE_AUTO_FLUSH &&
        ((deletesInRAM.size() + deletesFlushed.size()) >= maxBufferedDeleteTerms));
   }
@@ -1009,13 +1108,97 @@
   int getMaxBufferedDeleteTerms() {
     return maxBufferedDeleteTerms;
   }
-
+  
   synchronized boolean hasDeletes() {
-    return deletesFlushed.any();
+    if (deletesFlushed.any()) return true;
+    for (SegmentDeletes dels : segmentDeletes.values()) {
+      if (dels.any()) {
+        return true;
+      }
+    }
+    return false;
   }
+  
+  /**
+   * Apply deletes from the segment deletes map to individual readers.
+   */
+  synchronized boolean applyDeletesToSegments(SegmentInfos allInfos, int start, int length, MergePolicy.OneMerge merge) throws IOException {
+    IndexWriter.debug2("applyDeletesToSegments start:"+start+" length:"+length);
+    if (!hasDeletes())
+      return false;
+    
+    SegmentDeletes coalescedDeletes = null;
+    if (start > 0) {
+      coalescedDeletes = coalesceDeletes(allInfos, start, length);
+    }
+    
+    final long t0 = System.currentTimeMillis();
 
-  synchronized boolean applyDeletes(SegmentInfos infos) throws IOException {
+    if (infoStream != null)
+      message("apply " + deletesFlushed.numTerms + " buffered deleted terms and " +
+              deletesFlushed.docIDs.size() + " deleted docIDs and " +
+              deletesFlushed.queries.size() + " deleted queries on " +
+              + length + " segments.");
 
+    boolean any = false;
+    
+    for (int i = start; i < (length+start); i++) {
+      SegmentInfo info = allInfos.info(i);
+      // Make sure we never attempt to apply deletes to
+      // segment in external dir
+      assert info.dir == directory;
+      
+      SegmentDeletes deletes = getSegmentDeletes(i, allInfos);
+      
+      if (deletes != null) {
+        SegmentReader reader = writer.readerPool.get(info, false);
+        try {
+          any |= applyDeletesToSegment(deletes, reader);
+          
+          // the deletes that have been applied
+          // remove them from the segment deletes map
+          deletes.clear(this);
+          segmentDeletes.remove(info);
+        } finally {
+          writer.readerPool.release(reader);
+        }
+      }
+    }
+    if (infoStream != null) {
+      message("apply deletes took " + (System.currentTimeMillis()-t0) + " msec");
+    }
+    if (coalescedDeletes != null) {
+      assert start > 0;
+      SegmentInfo info = allInfos.get(start-1);
+      segmentDeletes.put(info, coalescedDeletes);
+    }
+    return any;
+  }
+  
+  /**
+   * If there's a (start - 1) segment, we merge deletes 
+   * from the segments up to (start + length).
+   */
+  synchronized SegmentDeletes coalesceDeletes(SegmentInfos allInfos, int start, int length) {
+    if (start > 0) {
+      int mergeSegIndex = start - 1;
+      SegmentInfo mergeSegInfo = allInfos.get(mergeSegIndex);
+      SegmentDeletes mergedDeletes = new SegmentDeletes(mergeSegInfo);
+      for (int x=lastSegmentIndex; x < (start+length); x++) {
+        SegmentInfo info = allInfos.get(x);
+        SegmentDeletes d = segmentDeletes.get(info);
+        if (d != null) {
+          mergedDeletes.addTerms(d.terms);
+          mergedDeletes.addQueries(d.queries);
+        }
+      }
+      return mergedDeletes;
+    }
+    return null;
+  }
+
+  synchronized boolean applyDeletesAll(SegmentInfos infos, int newLastSegmentIndex) throws IOException {
+
     if (!hasDeletes())
       return false;
 
@@ -1039,7 +1222,7 @@
 
       SegmentReader reader = writer.readerPool.get(infos.info(i), false);
       try {
-        any |= applyDeletes(reader, docStart);
+        any |= applyDeletesAllPerReader(reader, docStart);
         docStart += reader.maxDoc();
       } finally {
         writer.readerPool.release(reader);
@@ -1047,13 +1230,20 @@
     }
 
     deletesFlushed.clear();
+    
     if (infoStream != null) {
       message("apply deletes took " + (System.currentTimeMillis()-t0) + " msec");
     }
-
+    // because all pending deletes have now been applied
+    // clear out the pending per-segment deletes
+    for (SegmentDeletes d : segmentDeletes.values()) {
+      d.clear(this);
+    }
+    segmentDeletes.clear();
+    this.lastSegmentIndex = newLastSegmentIndex;
     return any;
   }
-
+  
   // used only by assert
   private Term lastDeleteTerm;
 
@@ -1065,10 +1255,88 @@
     lastDeleteTerm = term;
     return true;
   }
+  
+  private final synchronized boolean applyDeletesToSegment(SegmentDeletes deletes, SegmentReader reader) throws CorruptIndexException, IOException {
+    IndexWriter.debug2("applyDeletesToSegment seg:"+reader.getSegmentName());
+    boolean any = false;
 
+    assert checkDeleteTerm(null);
+
+    // Delete by term
+    if (deletes.terms.size() > 0) {
+      Fields fields = reader.fields();
+      if (fields == null) {
+        // This reader has no postings
+        return false;
+      }
+
+      TermsEnum termsEnum = null;
+      
+      String currentField = null;
+      DocsEnum docs = null;
+      
+      for (Term term : deletes.getSortedTerms()) {
+        // Since we visit terms sorted, we gain performance
+        // by re-using the same TermsEnum and seeking only
+        // forwards
+        if (term.field() != currentField) {
+          assert currentField == null || currentField.compareTo(term.field()) < 0;
+          currentField = term.field();
+          Terms terms = fields.terms(currentField);
+          if (terms != null) {
+            termsEnum = terms.iterator();
+          } else {
+            termsEnum = null;
+          }
+        }
+        
+        if (termsEnum == null) {
+          continue;
+        }
+        assert checkDeleteTerm(term);
+        
+        if (termsEnum.seek(term.bytes(), false) == TermsEnum.SeekStatus.FOUND) {
+          DocsEnum docsEnum = termsEnum.docs(reader.getDeletedDocs(), docs);
+          
+          if (docsEnum != null) {
+            docs = docsEnum;
+            while (true) {
+              final int docID = docs.nextDoc();
+              if (docID == DocsEnum.NO_MORE_DOCS) break;
+              reader.deleteDocument(docID);
+              any = true;
+            }
+          }
+        }
+      }
+    }
+
+    // Delete by query
+    if (deletes.queries.size() > 0) {
+      IndexSearcher searcher = new IndexSearcher(reader);
+      try {
+        for (Query query : deletes.queries) {
+          Weight weight = query.weight(searcher);
+          Scorer scorer = weight.scorer(reader, true, false);
+          if (scorer != null) {
+            while(true)  {
+              int doc = scorer.nextDoc();
+              if (doc == DocsEnum.NO_MORE_DOCS) break;
+              reader.deleteDocument(doc);
+              any = true;
+            }
+          }
+        }
+      } finally {
+        searcher.close();
+      }
+    }
+    return any;
+  }
+  
   // Apply buffered delete terms, queries and docIDs to the
   // provided reader
-  private final synchronized boolean applyDeletes(IndexReader reader, int docIDStart)
+  private final synchronized boolean applyDeletesAllPerReader(IndexReader reader, int docIDStart)
     throws CorruptIndexException, IOException {
 
     final int docEnd = docIDStart + reader.maxDoc();
@@ -1168,7 +1436,7 @@
   // current number of documents buffered in ram so that the
   // delete term will be applied to those documents as well
   // as the disk segments.
-  synchronized private void addDeleteTerm(Term term, int docCount) {
+  synchronized private void addDeleteTerm(Term term, int docCount, SegmentInfos infos) {
     BufferedDeletes.Num num = deletesInRAM.terms.get(term);
     final int docIDUpto = flushedDocCount + docCount;
     if (num == null)
@@ -1178,7 +1446,24 @@
     deletesInRAM.numTerms++;
 
     deletesInRAM.addBytesUsed(BYTES_PER_DEL_TERM + term.bytes.length);
+    
+    assert lastSegmentIndex >= 0;
+    
+    // add the delete term to the segments after lastSegmentIndex
+    for (int x=lastSegmentIndex; x < infos.size(); x++) {
+      SegmentInfo info = infos.get(x);
+      addDeleteTermToSegment(info, term);
+    }
   }
+  
+  synchronized void addDeleteTermToSegment(SegmentInfo info, Term term) {
+    SegmentDeletes dels = segmentDeletes.get(info);
+    if (dels == null) {
+      dels = new SegmentDeletes(info);
+      segmentDeletes.put(info, dels);
+    }
+    dels.addTerm(term);
+  }
 
   // Buffer a specific docID for deletion.  Currently only
   // used when we hit a exception when adding a document
@@ -1187,9 +1472,22 @@
     deletesInRAM.addBytesUsed(BYTES_PER_DEL_DOCID);
   }
 
-  synchronized private void addDeleteQuery(Query query, int docID) {
+  synchronized private void addDeleteQuery(Query query, int docID, SegmentInfos infos) {
     deletesInRAM.queries.put(query, Integer.valueOf(flushedDocCount + docID));
     deletesInRAM.addBytesUsed(BYTES_PER_DEL_QUERY);
+    
+    assert lastSegmentIndex >= 0;
+    
+    // add the delete query to the segments after lastSegmentIndex
+    for (int x=lastSegmentIndex; x < infos.size(); x++) {
+      SegmentInfo info = infos.get(x);
+      SegmentDeletes dels = segmentDeletes.get(info);
+      if (dels == null) {
+        dels = new SegmentDeletes(info);
+        segmentDeletes.put(info, dels);
+      }
+      dels.queries.add(query);
+    }
   }
 
   /** Does the synchronized work to finish/flush the
@@ -1373,7 +1671,7 @@
         return;
       }
     
-      deletesRAMUsed = deletesInRAM.bytesUsed+deletesFlushed.bytesUsed;
+      deletesRAMUsed = deletesInRAM.bytesUsed+deletesFlushed.bytesUsed+segmentDeletesBytesUsed.get();
       doBalance = bytesUsed() +deletesRAMUsed >= ramBufferSize;
     }
 
Index: src/java/org/apache/lucene/index/IndexWriter.java
===================================================================
--- src/java/org/apache/lucene/index/IndexWriter.java	(revision 1030113)
+++ src/java/org/apache/lucene/index/IndexWriter.java	(working copy)
@@ -30,6 +30,7 @@
 import org.apache.lucene.store.BufferedIndexInput;
 import org.apache.lucene.util.Constants;
 import org.apache.lucene.index.codecs.CodecProvider;
+import org.apache.lucene.index.DocumentsWriter.SegmentDeletes;
 import org.apache.lucene.util.ThreadInterruptedException;
 import org.apache.lucene.util.Version;
 import org.apache.lucene.util.Bits;
@@ -279,9 +280,9 @@
   volatile SegmentInfos pendingCommit;            // set when a commit is pending (after prepareCommit() & before commit())
   volatile long pendingCommitChangeCount;
 
-  private SegmentInfos segmentInfos = new SegmentInfos();       // the segments
+  SegmentInfos segmentInfos = new SegmentInfos();       // the segments
 
-  private DocumentsWriter docWriter;
+  DocumentsWriter docWriter;
   private IndexFileDeleter deleter;
 
   private Set<SegmentInfo> segmentsToOptimize = new HashSet<SegmentInfo>();           // used by optimize to note those needing optimization
@@ -329,7 +330,14 @@
 
   // The PayloadProcessorProvider to use when segments are merged
   private PayloadProcessorProvider payloadProcessorProvider;
-
+  
+  static PrintStream debug2 = null;
+  static void debug2(String msg) {
+    if (debug2 != null) {
+      debug2.println(msg);
+    }
+  }
+  
   /**
    * Expert: returns a readonly reader, covering all
    * committed as well as un-committed changes to the index.
@@ -408,7 +416,7 @@
     // reader; in theory we could do similar retry logic,
     // just like we do when loading segments_N
     synchronized(this) {
-      applyDeletes();
+      applyDeletesAll();
       final IndexReader r = new DirectoryReader(this, segmentInfos, config.getReaderTermsIndexDivisor(), codecs);
       if (infoStream != null) {
         message("return reader version=" + r.getVersion() + " reader=" + r);
@@ -1106,13 +1114,11 @@
             message("init: loaded commit \"" + commit.getSegmentsFileName() + "\"");
         }
       }
-
       setRollbackSegmentInfos(segmentInfos);
 
       docWriter = new DocumentsWriter(directory, this, conf.getIndexingChain(), conf.getMaxThreadStates());
       docWriter.setInfoStream(infoStream);
       docWriter.setMaxFieldLength(maxFieldLength);
-
       // Default deleter (for backwards compatibility) is
       // KeepOnlyLastCommitDeleter:
       deleter = new IndexFileDeleter(directory,
@@ -2001,7 +2007,19 @@
   public void addDocument(Document doc) throws CorruptIndexException, IOException {
     addDocument(doc, analyzer);
   }
-
+  
+  synchronized SegmentInfos getSegmentInfos(boolean copy) {
+    if (copy) {
+      SegmentInfos copiedInfos = new SegmentInfos();
+      for (SegmentInfo info : segmentInfos) {
+        copiedInfos.add(info);
+      }
+      return copiedInfos;
+    } else {
+      return segmentInfos;
+    }
+  }
+  
   /**
    * Adds a document to this index, using the provided analyzer instead of the
    * value of {@link #getAnalyzer()}.  If the document contains more than
@@ -2025,7 +2043,7 @@
     boolean success = false;
     try {
       try {
-        doFlush = docWriter.addDocument(doc, analyzer);
+        doFlush = docWriter.addDocument(doc, analyzer, getSegmentInfos(true));
         success = true;
       } finally {
         if (!success) {
@@ -2065,7 +2083,7 @@
   public void deleteDocuments(Term term) throws CorruptIndexException, IOException {
     ensureOpen();
     try {
-      boolean doFlush = docWriter.bufferDeleteTerm(term);
+      boolean doFlush = docWriter.bufferDeleteTerm(term, getSegmentInfos(true));
       if (doFlush)
         flush(true, false, false);
     } catch (OutOfMemoryError oom) {
@@ -2089,7 +2107,7 @@
   public void deleteDocuments(Term... terms) throws CorruptIndexException, IOException {
     ensureOpen();
     try {
-      boolean doFlush = docWriter.bufferDeleteTerms(terms);
+      boolean doFlush = docWriter.bufferDeleteTerms(terms, getSegmentInfos(true));
       if (doFlush)
         flush(true, false, false);
     } catch (OutOfMemoryError oom) {
@@ -2110,7 +2128,7 @@
    */
   public void deleteDocuments(Query query) throws CorruptIndexException, IOException {
     ensureOpen();
-    boolean doFlush = docWriter.bufferDeleteQuery(query);
+    boolean doFlush = docWriter.bufferDeleteQuery(query, getSegmentInfos(true));
     if (doFlush)
       flush(true, false, false);
   }
@@ -2130,7 +2148,7 @@
    */
   public void deleteDocuments(Query... queries) throws CorruptIndexException, IOException {
     ensureOpen();
-    boolean doFlush = docWriter.bufferDeleteQueries(queries);
+    boolean doFlush = docWriter.bufferDeleteQueries(queries, getSegmentInfos(true));
     if (doFlush)
       flush(true, false, false);
   }
@@ -2182,7 +2200,7 @@
       boolean doFlush = false;
       boolean success = false;
       try {
-        doFlush = docWriter.updateDocument(term, doc, analyzer);
+        doFlush = docWriter.updateDocument(term, doc, analyzer, getSegmentInfos(true));
         success = true;
       } finally {
         if (!success) {
@@ -3401,7 +3419,7 @@
       }
 
       if (flushDeletes) {
-        applyDeletes();
+        applyDeletesAll();
       }
       
       if (flushDocs)
@@ -3569,14 +3587,14 @@
 
     commitMergedDeletes(merge, mergedReader);
     docWriter.remapDeletes(segmentInfos, merger.getDocMaps(), merger.getDelCounts(), merge, mergedDocCount);
-      
+    
     setMergeDocStoreIsCompoundFile(merge);
     merge.info.setHasProx(merger.hasProx());
-
+    
     segmentInfos.subList(start, start + merge.segments.size()).clear();
     assert !segmentInfos.contains(merge.info);
     segmentInfos.add(start, merge.info);
-
+    
     // Must note the change to segmentInfos so any commits
     // in-flight don't lose it:
     checkpoint();
@@ -3683,6 +3701,7 @@
 
   /** Hook that's called when the specified merge is complete. */
   void mergeSuccess(MergePolicy.OneMerge merge) {
+    
   }
   
   /** Checks whether this merge involves any segments
@@ -3767,11 +3786,14 @@
     if (merge.isAborted())
       return;
 
-    applyDeletes();
-
     final SegmentInfos sourceSegments = merge.segments;
+    
+    int start = ensureContiguousMerge(merge);
+    
     final int end = sourceSegments.size();
-
+        
+    docWriter.applyDeletesToSegments(segmentInfos, start, end, merge);
+        
     // Check whether this merge will allow us to skip
     // merging the doc stores (stored field & vectors).
     // This is a very substantial optimization (saves tons
@@ -3935,7 +3957,7 @@
       mergingSegments.remove(merge.info);
       merge.registerDone = false;
     }
-
+    
     runningMerges.remove(merge);
   }
 
@@ -4225,7 +4247,7 @@
   }
 
   // Apply buffered deletes to all segments.
-  private final synchronized boolean applyDeletes() throws CorruptIndexException, IOException {
+  private final synchronized boolean applyDeletesAll() throws CorruptIndexException, IOException {
     assert testPoint("startApplyDeletes");
     if (infoStream != null) {
       message("applyDeletes");
@@ -4234,7 +4256,7 @@
     boolean success = false;
     boolean changed;
     try {
-      changed = docWriter.applyDeletes(segmentInfos);
+      changed = docWriter.applyDeletesAll(segmentInfos, segmentInfos.size()-1);
       success = true;
     } finally {
       if (!success && infoStream != null) {
