Index: lucene/queryparser/src/test/org/apache/lucene/queryparser/flexible/precedence/TestPrecedenceQueryParser.java
===================================================================
--- lucene/queryparser/src/test/org/apache/lucene/queryparser/flexible/precedence/TestPrecedenceQueryParser.java	(revision 1530072)
+++ lucene/queryparser/src/test/org/apache/lucene/queryparser/flexible/precedence/TestPrecedenceQueryParser.java	(working copy)
@@ -29,8 +29,8 @@
 import java.util.TimeZone;
 
 import org.apache.lucene.analysis.*;
+import org.apache.lucene.analysis.tokenattributes.CharTermAttribute;
 import org.apache.lucene.analysis.tokenattributes.OffsetAttribute;
-import org.apache.lucene.analysis.tokenattributes.CharTermAttribute;
 import org.apache.lucene.document.DateTools;
 import org.apache.lucene.queryparser.flexible.core.QueryNodeException;
 import org.apache.lucene.queryparser.flexible.core.QueryNodeParseException;
@@ -48,6 +48,8 @@
 import org.apache.lucene.util.LuceneTestCase;
 import org.apache.lucene.util.automaton.BasicAutomata;
 import org.apache.lucene.util.automaton.CharacterRunAutomaton;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 
 /**
  * <p>
@@ -64,8 +66,18 @@
 //that it adjusts to fit the precedence requirement, adding its extra tests.
 public class TestPrecedenceQueryParser extends LuceneTestCase {
 
-  public static Analyzer qpAnalyzer = new QPTestAnalyzer();
+  public static Analyzer qpAnalyzer;
 
+  @BeforeClass
+  public static void beforeClass() {
+    qpAnalyzer = new QPTestAnalyzer();
+  }
+
+  @AfterClass
+  public static void afterClass() {
+    qpAnalyzer = null;
+  }
+
   public static final class QPTestFilter extends TokenFilter {
     /**
      * Filter which discards the token 'stop' and which expands the token
Index: lucene/queryparser/src/test/org/apache/lucene/queryparser/flexible/standard/TestQPHelper.java
===================================================================
--- lucene/queryparser/src/test/org/apache/lucene/queryparser/flexible/standard/TestQPHelper.java	(revision 1530072)
+++ lucene/queryparser/src/test/org/apache/lucene/queryparser/flexible/standard/TestQPHelper.java	(working copy)
@@ -70,6 +70,8 @@
 import org.apache.lucene.util.automaton.BasicAutomata;
 import org.apache.lucene.util.automaton.CharacterRunAutomaton;
 import org.apache.lucene.util.automaton.RegExp;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 import org.junit.Ignore;
 
 /**
@@ -81,8 +83,18 @@
 // TODO: really this should extend QueryParserTestBase too!
 public class TestQPHelper extends LuceneTestCase {
 
-  public static Analyzer qpAnalyzer = new QPTestAnalyzer();
+  public static Analyzer qpAnalyzer;
 
+  @BeforeClass
+  public static void beforeClass() {
+    qpAnalyzer = new QPTestAnalyzer();
+  }
+
+  @AfterClass
+  public static void afterClass() {
+    qpAnalyzer = null;
+  }
+
   public static final class QPTestFilter extends TokenFilter {
     private final CharTermAttribute termAtt = addAttribute(CharTermAttribute.class);
     private final OffsetAttribute offsetAtt = addAttribute(OffsetAttribute.class);
Index: lucene/queryparser/src/test/org/apache/lucene/queryparser/util/QueryParserTestBase.java
===================================================================
--- lucene/queryparser/src/test/org/apache/lucene/queryparser/util/QueryParserTestBase.java	(revision 1530072)
+++ lucene/queryparser/src/test/org/apache/lucene/queryparser/util/QueryParserTestBase.java	(working copy)
@@ -41,8 +41,8 @@
 //import org.apache.lucene.queryparser.classic.ParseException;
 //import org.apache.lucene.queryparser.classic.QueryParser;
 //import org.apache.lucene.queryparser.classic.QueryParserBase;
+import org.apache.lucene.queryparser.classic.QueryParserBase;
 //import org.apache.lucene.queryparser.classic.QueryParserTokenManager;
-import org.apache.lucene.queryparser.classic.QueryParserBase;
 import org.apache.lucene.queryparser.flexible.standard.CommonQueryParserConfiguration;
 import org.apache.lucene.search.*;
 import org.apache.lucene.search.BooleanClause.Occur;
@@ -51,6 +51,8 @@
 import org.apache.lucene.util.automaton.BasicAutomata;
 import org.apache.lucene.util.automaton.CharacterRunAutomaton;
 import org.apache.lucene.util.automaton.RegExp;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
 
 /**
  * Base Test class for QueryParser subclasses
@@ -59,8 +61,18 @@
 // to the core QP and subclass/use the parts that are not in the flexible QP
 public abstract class QueryParserTestBase extends LuceneTestCase {
   
-  public static Analyzer qpAnalyzer = new QPTestAnalyzer();
+  public static Analyzer qpAnalyzer;
 
+  @BeforeClass
+  public static void beforeClass() {
+    qpAnalyzer = new QPTestAnalyzer();
+  }
+
+  @AfterClass
+  public static void afterClass() {
+    qpAnalyzer = null;
+  }
+  
   public static final class QPTestFilter extends TokenFilter {
     CharTermAttribute termAtt;
     OffsetAttribute offsetAtt;
@@ -102,7 +114,6 @@
     }
   }
 
-  
   public static final class QPTestAnalyzer extends Analyzer {
 
     /** Filters MockTokenizer with StopFilter. */
Index: lucene/core/src/test/org/apache/lucene/index/TestIndexWriterReader.java
===================================================================
--- lucene/core/src/test/org/apache/lucene/index/TestIndexWriterReader.java	(revision 1530072)
+++ lucene/core/src/test/org/apache/lucene/index/TestIndexWriterReader.java	(working copy)
@@ -35,6 +35,7 @@
 import org.apache.lucene.search.TopDocs;
 import org.apache.lucene.store.AlreadyClosedException;
 import org.apache.lucene.store.Directory;
+import org.apache.lucene.store.MockDirectoryWrapper.FakeIOException;
 import org.apache.lucene.store.MockDirectoryWrapper;
 import org.apache.lucene.store.RAMDirectory;
 import org.apache.lucene.util.BytesRef;
@@ -157,6 +158,7 @@
     assertEquals(1, count(new Term("id", Integer.toString(8000)), r2));
     
     r1.close();
+    assertTrue(r2.isCurrent());
     writer.close();
     assertTrue(r2.isCurrent());
     
@@ -1042,10 +1044,6 @@
     d.close();
   }
   
-  private static final class FakeIOException extends IOException {
-    public FakeIOException() {}
-  }
-  
   @Test
   public void testNRTOpenExceptions() throws Exception {
     // LUCENE-5262: test that several failed attempts to obtain an NRT reader
Index: lucene/core/src/test/org/apache/lucene/index/TestIndexWriter.java
===================================================================
--- lucene/core/src/test/org/apache/lucene/index/TestIndexWriter.java	(revision 1530072)
+++ lucene/core/src/test/org/apache/lucene/index/TestIndexWriter.java	(working copy)
@@ -1025,13 +1025,23 @@
     @Override
     public void run() {
       // LUCENE-2239: won't work with NIOFS/MMAP
-      Directory dir = new MockDirectoryWrapper(random, new RAMDirectory());
+      MockDirectoryWrapper dir = new MockDirectoryWrapper(random, new RAMDirectory());
+
+      // When interrupt arrives in w.close(), when it's
+      // writing liveDocs, this can lead to double-write of
+      // _X_N.del:
+      //dir.setPreventDoubleWrite(false);
       IndexWriter w = null;
       while(!finish) {
         try {
 
           while(!finish) {
             if (w != null) {
+              // If interrupt arrives inside here, it's
+              // fine: we will cycle back and the first
+              // thing we do is try to close again,
+              // i.e. we'll never try to open a new writer
+              // until this one successfully closes:
               w.close();
               w = null;
             }
Index: lucene/core/src/test/org/apache/lucene/index/TestIndexWriterDelete.java
===================================================================
--- lucene/core/src/test/org/apache/lucene/index/TestIndexWriterDelete.java	(revision 1530072)
+++ lucene/core/src/test/org/apache/lucene/index/TestIndexWriterDelete.java	(working copy)
@@ -40,6 +40,7 @@
 import org.apache.lucene.search.ScoreDoc;
 import org.apache.lucene.search.TermQuery;
 import org.apache.lucene.store.Directory;
+import org.apache.lucene.store.MockDirectoryWrapper.FakeIOException;
 import org.apache.lucene.store.MockDirectoryWrapper;
 import org.apache.lucene.store.RAMDirectory;
 import org.apache.lucene.util.LuceneTestCase;
@@ -322,7 +323,7 @@
           int value = 100;
           try {
             latch.await();
-            for (int i = 0; i < 1000; i++) {
+            for (int j = 0; j < 1000; j++) {
               Document doc = new Document();
               doc.add(newTextField("content", "aaa", Field.Store.NO));
               doc.add(newStringField("id", String.valueOf(id++), Field.Store.YES));
@@ -1218,13 +1219,11 @@
     d.close();
   }
 
-  private static class FakeIOException extends IOException {
-  }
-
-  // Make sure if we hit disk full, and then later disk
-  // frees up, and we successfully close IW or open an NRT
+  // Make sure if we hit a transient IOException (e.g., disk
+  // full), and then the exception stops (e.g., disk frees
+  // up), so we successfully close IW or open an NRT
   // reader, we don't lose any deletes:
-  public void testNoLostDeletesOnDiskFull() throws Exception {
+  public void testNoLostDeletesOnIOException() throws Exception {
 
     int deleteCount = 0;
     int docBase = 0;
@@ -1237,35 +1236,70 @@
           @Override
           public void eval(MockDirectoryWrapper dir) throws IOException {
             StackTraceElement[] trace = new Exception().getStackTrace();
-            if (shouldFail.get()) {
-              for (int i = 0; i < trace.length; i++) {
-                if ("writeLiveDocs".equals(trace[i].getMethodName())) {
-                  // Only sometimes throw the exc, so we get
-                  // it sometimes on creating the file, on
-                  // flushing buffer, on closing the file:
-                  if (random().nextInt(3) == 2) {
-                    if (VERBOSE) {
-                      System.out.println("TEST: now fail; exc:");
-                      new Throwable().printStackTrace(System.out);
-                    }
-                    shouldFail.set(false);
-                    throw new FakeIOException();
-                  } else {
-                    break;
-                  }
-                }
+            if (shouldFail.get() == false) {
+              return;
+            }
+
+            boolean sawSeal = false;
+            boolean sawWrite = false;
+            for (int i = 0; i < trace.length; i++) {
+              if ("sealFlushedSegment".equals(trace[i].getMethodName())) {
+                sawSeal = true;
+                break;
               }
+              if ("writeLiveDocs".equals(trace[i].getMethodName())) {
+                sawWrite = true;
+              }
             }
+
+            // Don't throw exc if we are "flushing", else
+            // the segment is aborted and docs are lost:
+            if (sawWrite && sawSeal == false && random().nextInt(3) == 2) {
+              // Only sometimes throw the exc, so we get
+              // it sometimes on creating the file, on
+              // flushing buffer, on closing the file:
+              if (VERBOSE) {
+                System.out.println("TEST: now fail; thread=" + Thread.currentThread().getName() + " exc:");
+                new Throwable().printStackTrace(System.out);
+              }
+              shouldFail.set(false);
+              throw new FakeIOException();
+            }
           }
       });
 
+    RandomIndexWriter w = null;
+
     for(int iter=0;iter<10*RANDOM_MULTIPLIER;iter++) {
       int numDocs = atLeast(100);
       if (VERBOSE) {
-        System.out.println("\nTEST: iter=" + iter + " numDocs=" + numDocs + " docBase=" + docBase);
+        System.out.println("\nTEST: iter=" + iter + " numDocs=" + numDocs + " docBase=" + docBase + " delCount=" + deleteCount);
       }
-      IndexWriterConfig iwc = newIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(random()));
-      IndexWriter w = new IndexWriter(dir, iwc);
+      if (w == null) {
+        IndexWriterConfig iwc = newIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(random()));
+        final MergeScheduler ms = iwc.getMergeScheduler();
+        if (ms instanceof ConcurrentMergeScheduler) {
+          final ConcurrentMergeScheduler suppressFakeIOE = new ConcurrentMergeScheduler() {
+              @Override
+              protected void handleMergeException(Throwable exc) {
+                // suppress only FakeIOException:
+                if (!(exc instanceof FakeIOException)) {
+                  super.handleMergeException(exc);
+                }
+              }
+            };
+          final ConcurrentMergeScheduler cms = (ConcurrentMergeScheduler) ms;
+          suppressFakeIOE.setMaxMergesAndThreads(cms.getMaxMergeCount(), cms.getMaxThreadCount());
+          suppressFakeIOE.setMergeThreadPriority(cms.getMergeThreadPriority());
+          iwc.setMergeScheduler(suppressFakeIOE);
+          iwc.setMergeScheduler(suppressFakeIOE);
+        }
+        w = new RandomIndexWriter(random(), dir, iwc);
+        // Since we hit exc during merging, a partial
+        // forceMerge can easily return when there are still
+        // too many segments in the index:
+        w.setDoRandomForceMergeAssert(false);
+      }
       for(int i=0;i<numDocs;i++) {
         Document doc = new Document();
         doc.add(new StringField("id", ""+(docBase+i), Field.Store.NO));
@@ -1273,9 +1307,8 @@
       }
       docCount += numDocs;
 
-      IndexReader r = w.getReader();
-      assertEquals(docCount-deleteCount, r.numDocs());
-      r.close();
+      // TODO: we could make the test more evil, by letting
+      // it throw more than one exc, randomly, before "recovering"
 
       // TODO: we could also install an infoStream and try
       // to fail in "more evil" places inside BDS
@@ -1286,29 +1319,74 @@
 
         for(int i=0;i<numDocs;i++) {
           if (random().nextInt(10) == 7) {
+            if (VERBOSE) {
+              System.out.println("  delete id=" + (docBase+i));
+            }
             deleteCount++;
             w.deleteDocuments(new Term("id", ""+(docBase+i)));
           }
         }
 
-        w.close();
+        // Trigger writeLiveDocs so we hit fake exc:
+        IndexReader r = w.getReader(true);
+
+        // Sometimes we will make it here (we only randomly
+        // throw the exc):
+        assertEquals(docCount-deleteCount, r.numDocs());
+        r.close();
+
+        // TODO: also call w.close() in here, sometimes,
+        // so we sometimes get a fail via dropAll
+
       } catch (FakeIOException ioe) {
         // expected
         if (VERBOSE) {
           System.out.println("TEST: w.close() hit expected IOE");
         }
         // No exception should happen here (we only fail once):
-        w.close();
       }
       shouldFail.set(false);
 
-      r = DirectoryReader.open(dir);
+      IndexReader r;
+
+      if (random().nextBoolean()) {
+        // Open non-NRT reader, to make sure the "on
+        // disk" bits are good:
+        if (VERBOSE) {
+          System.out.println("TEST: verify against non-NRT reader");
+        }
+        w.commit();
+        r = DirectoryReader.open(dir);
+      } else {
+        if (VERBOSE) {
+          System.out.println("TEST: verify against NRT reader");
+        }
+        r = w.getReader();
+      }
       assertEquals(docCount-deleteCount, r.numDocs());
       r.close();
 
+      // Sometimes re-use RIW, other times open new one:
+      if (random().nextBoolean()) {
+        if (VERBOSE) {
+          System.out.println("TEST: close writer");
+        }
+        w.close();
+        w = null;
+      }
+
       docBase += numDocs;
     }
 
+    if (w != null) {
+      w.close();
+    }
+
+    // Final verify:
+    IndexReader r = DirectoryReader.open(dir);
+    assertEquals(docCount-deleteCount, r.numDocs());
+    r.close();
+
     dir.close();
   }
 }
Index: lucene/core/src/java/org/apache/lucene/index/StandardDirectoryReader.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/index/StandardDirectoryReader.java	(revision 1530072)
+++ lucene/core/src/java/org/apache/lucene/index/StandardDirectoryReader.java	(working copy)
@@ -61,8 +61,9 @@
           } catch(IOException ex) {
             prior = ex;
           } finally {
-            if (!success)
+            if (!success) {
               IOUtils.closeWhileHandlingException(prior, readers);
+            }
           }
         }
         return new StandardDirectoryReader(directory, readers, null, sis, false);
@@ -214,12 +215,7 @@
           }
         }
         // throw the first exception
-        if (prior != null) {
-          if (prior instanceof IOException) throw (IOException) prior;
-          if (prior instanceof RuntimeException) throw (RuntimeException) prior;
-          if (prior instanceof Error) throw (Error) prior;
-          throw new RuntimeException(prior);
-        }
+        IOUtils.reThrow(prior);
       }
     }    
     return new StandardDirectoryReader(directory, newReaders, null, infos, false);
@@ -359,7 +355,9 @@
       try {
         r.decRef();
       } catch (Throwable t) {
-        if (firstExc == null) firstExc = t;
+        if (firstExc == null) {
+          firstExc = t;
+        }
       }
     }
 
@@ -370,12 +368,7 @@
     }
 
     // throw the first exception
-    if (firstExc != null) {
-      if (firstExc instanceof IOException) throw (IOException) firstExc;
-      if (firstExc instanceof RuntimeException) throw (RuntimeException) firstExc;
-      if (firstExc instanceof Error) throw (Error) firstExc;
-      throw new RuntimeException(firstExc);
-    }
+    IOUtils.reThrow(firstExc);
   }
 
   @Override
Index: lucene/core/src/java/org/apache/lucene/index/SegmentReader.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/index/SegmentReader.java	(revision 1530072)
+++ lucene/core/src/java/org/apache/lucene/index/SegmentReader.java	(working copy)
@@ -21,8 +21,8 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map.Entry;
 import java.util.Map;
-import java.util.Map.Entry;
 
 import org.apache.lucene.codecs.Codec;
 import org.apache.lucene.codecs.DocValuesFormat;
@@ -36,6 +36,7 @@
 import org.apache.lucene.store.IOContext;
 import org.apache.lucene.util.Bits;
 import org.apache.lucene.util.CloseableThreadLocal;
+import org.apache.lucene.util.IOUtils;
 import org.apache.lucene.util.RefCount;
 
 /**
@@ -313,12 +314,7 @@
       dvProducers.clear();
       docValuesLocal.close();
       docsWithFieldLocal.close();
-      if (t != null) {
-        if (t instanceof IOException) throw (IOException) t;
-        if (t instanceof RuntimeException) throw (RuntimeException) t;
-        if (t instanceof Error) throw (Error) t;
-        throw new RuntimeException(t);
-      }
+      IOUtils.reThrow(t);
     }
   }
 
Index: lucene/core/src/java/org/apache/lucene/index/SegmentInfoPerCommit.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/index/SegmentInfoPerCommit.java	(revision 1530072)
+++ lucene/core/src/java/org/apache/lucene/index/SegmentInfoPerCommit.java	(working copy)
@@ -230,12 +230,7 @@
 
   /** Returns a description of this segment. */
   public String toString(Directory dir, int pendingDelCount) {
-    return info.toString(dir, delCount + pendingDelCount);
-  }
-
-  @Override
-  public String toString() {
-    String s = info.toString(info.dir, delCount);
+    String s = info.toString(dir, delCount + pendingDelCount);
     if (delGen != -1) {
       s += ":delGen=" + delGen;
     }
@@ -246,6 +241,11 @@
   }
 
   @Override
+  public String toString() {
+    return toString(info.dir, 0);
+  }
+
+  @Override
   public SegmentInfoPerCommit clone() {
     SegmentInfoPerCommit other = new SegmentInfoPerCommit(info, delCount, delGen, fieldInfosGen);
     // Not clear that we need to carry over nextWriteDelGen
Index: lucene/core/src/java/org/apache/lucene/index/IndexWriter.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/index/IndexWriter.java	(revision 1530072)
+++ lucene/core/src/java/org/apache/lucene/index/IndexWriter.java	(working copy)
@@ -450,7 +450,11 @@
     }
 
     public synchronized void release(ReadersAndLiveDocs rld) throws IOException {
+      release(rld, true);
+    }
 
+    public synchronized void release(ReadersAndLiveDocs rld, boolean assertInfoLive) throws IOException {
+
       // Matches incRef in get:
       rld.decRef();
 
@@ -463,11 +467,17 @@
 //        System.out.println("[" + Thread.currentThread().getName() + "] ReaderPool.release: " + rld.info);
         if (rld.writeLiveDocs(directory)) {
           // Make sure we only write del docs and field updates for a live segment:
-          assert infoIsLive(rld.info);
-          // Must checkpoint w/ deleter, because we just
-          // created new _X_N.del and field updates files.
-          deleter.checkpoint(segmentInfos, false);
+          assert assertInfoLive == false || infoIsLive(rld.info);
+          // Must checkpoint because we just
+          // created new _X_N.del and field updates files;
+          // don't call IW.checkpoint because that also
+          // increments SIS.version, which we do not want to
+          // do here: it was done previously (after we
+          // invoked BDS.applyDeletes), whereas here all we
+          // did was move the state to disk:
+          checkpointNoSIS();
         }
+        //System.out.println("IW: done writeLiveDocs for info=" + rld.info);
 
 //        System.out.println("[" + Thread.currentThread().getName() + "] ReaderPool.release: drop readers " + rld.info);
         rld.dropReaders();
@@ -487,12 +497,19 @@
           if (doSave && rld.writeLiveDocs(directory)) {
             // Make sure we only write del docs and field updates for a live segment:
             assert infoIsLive(rld.info);
-            // Must checkpoint w/ deleter, because we just
-            // created created new _X_N.del and field updates files.
-            deleter.checkpoint(segmentInfos, false);
+            // Must checkpoint because we just
+            // created new _X_N.del and field updates files;
+            // don't call IW.checkpoint because that also
+            // increments SIS.version, which we do not want to
+            // do here: it was done previously (after we
+            // invoked BDS.applyDeletes), whereas here all we
+            // did was move the state to disk:
+            checkpointNoSIS();
           }
         } catch (Throwable t) {
-          if (priorE != null) {
+          if (doSave) {
+            IOUtils.reThrow(t);
+          } else if (priorE == null) {
             priorE = t;
           }
         }
@@ -510,15 +527,15 @@
         try {
           rld.dropReaders();
         } catch (Throwable t) {
-          if (priorE != null) {
+          if (doSave) {
+            IOUtils.reThrow(t);
+          } else if (priorE == null) {
             priorE = t;
           }
         }
       }
       assert readerMap.size() == 0;
-      if (priorE != null) {
-        throw new RuntimeException(priorE);
-      }
+      IOUtils.reThrow(priorE);
     }
 
     /**
@@ -537,10 +554,16 @@
             // Make sure we only write del docs and updates for a live segment:
             assert infoIsLive(info);
 
-            // Must checkpoint w/ deleter, because we just
-            // created new _X_N.del and field updates files.
+            // Must checkpoint because we just
+            // created new _X_N.del and field updates files;
+            // don't call IW.checkpoint because that also
+            // increments SIS.version, which we do not want to
+            // do here: it was done previously (after we
+            // invoked BDS.applyDeletes), whereas here all we
+            // did was move the state to disk:
             deleter.checkpoint(segmentInfos, false);
-            
+            checkpointNoSIS();
+
             // we wrote field updates, reopen the reader
             if (hasFieldUpdates) {
               rld.reopenReader(IOContext.READ);
@@ -1005,21 +1028,32 @@
         infoStream.message("IW", "now call final commit()");
       }
 
+      // Must do this before commitInternal, in case any of
+      // the dropped readers in the pool wrote a new live
+      // docs: 
+      synchronized(this) {
+        readerPool.dropAll(true);
+      }
+
       if (doFlush) {
         commitInternal();
       }
 
-      if (infoStream.isEnabled("IW")) {
-        infoStream.message("IW", "at close: " + segString());
+      synchronized(this) {
+        deleter.close();
       }
+
       // used by assert below
       final DocumentsWriter oldWriter = docWriter;
-      synchronized(this) {
-        readerPool.dropAll(true);
+
+      synchronized (this) {
         docWriter = null;
-        deleter.close();
       }
 
+      if (infoStream.isEnabled("IW")) {
+        infoStream.message("IW", "at close: " + segString());
+      }
+
       if (writeLock != null) {
         writeLock.release();                          // release write lock
         writeLock = null;
@@ -2259,6 +2293,15 @@
     deleter.checkpoint(segmentInfos, false);
   }
 
+  /** Checkpoints with IndexFileDeleter, so it's aware of
+   *  new files, and increments changeCount, so on
+   *  close/commit we will write a new segments file, but
+   *  does NOT bump segmentInfos.version. */
+  synchronized void checkpointNoSIS() throws IOException {
+    changeCount++;
+    deleter.checkpoint(segmentInfos, false);
+  }
+
   /** Called internally if any index state has changed. */
   synchronized void changed() {
     changeCount++;
@@ -2911,6 +2954,8 @@
         segmentInfos.updateGeneration(pendingCommit);
         lastCommitChangeCount = pendingCommitChangeCount;
         rollbackSegments = pendingCommit.createBackupSegmentInfos();
+        // NOTE: don't use this.checkpoint() here, because
+        // we do not want to increment changeCount:
         deleter.checkpoint(pendingCommit, true);
       } finally {
         // Matches the incRef done in prepareCommit:
@@ -3334,16 +3379,22 @@
 
     assert merge.info.info.getDocCount() != 0 || keepFullyDeletedSegments || dropSegment;
 
-    segmentInfos.applyMergeChanges(merge, dropSegment);
-
     if (mergedDeletes != null) {
       if (dropSegment) {
-//        System.out.println("[" + Thread.currentThread().getName() + "] IW.commitMerge: dropChanges " + merge.info);
         mergedDeletes.dropChanges();
       }
-      readerPool.release(mergedDeletes);
+      // Pass false for assertInfoLive because the merged
+      // segment is not yet live (only below do we commit it
+      // to the segmentInfos):
+      readerPool.release(mergedDeletes, false);
     }
 
+    // Must do this after readerPool.release, in case an
+    // exception is hit e.g. writing the live docs for the
+    // merge segment, in which case we need to abort the
+    // merge:
+    segmentInfos.applyMergeChanges(merge, dropSegment);
+
     if (dropSegment) {
       assert !segmentInfos.contains(merge.info);
       readerPool.drop(merge.info);
@@ -3407,17 +3458,12 @@
       // in which case we must throw it so, for example, the
       // rollbackTransaction code in addIndexes* is
       // executed.
-      if (merge.isExternal)
+      if (merge.isExternal) {
         throw (MergePolicy.MergeAbortedException) t;
-    } else if (t instanceof IOException)
-      throw (IOException) t;
-    else if (t instanceof RuntimeException)
-      throw (RuntimeException) t;
-    else if (t instanceof Error)
-      throw (Error) t;
-    else
-      // Should not get here
-      throw new RuntimeException(t);
+      }
+    } else {
+      IOUtils.reThrow(t);
+    }
   }
 
   /**
@@ -3736,11 +3782,8 @@
     }
     
     // If any error occured, throw it.
-    if (!suppressExceptions && th != null) {
-      if (th instanceof IOException) throw (IOException) th;
-      if (th instanceof RuntimeException) throw (RuntimeException) th;
-      if (th instanceof Error) throw (Error) th;
-      throw new RuntimeException(th);
+    if (!suppressExceptions) {
+      IOUtils.reThrow(th);
     }
   }
 
Index: lucene/core/src/java/org/apache/lucene/util/IOUtils.java
===================================================================
--- lucene/core/src/java/org/apache/lucene/util/IOUtils.java	(revision 1530072)
+++ lucene/core/src/java/org/apache/lucene/util/IOUtils.java	(working copy)
@@ -26,7 +26,6 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
-import java.lang.reflect.Method;
 import java.nio.charset.Charset;
 import java.nio.charset.CharsetDecoder;
 import java.nio.charset.CodingErrorAction;
@@ -90,11 +89,8 @@
 
     if (priorException != null) {
       throw priorException;
-    } else if (th != null) {
-      if (th instanceof IOException) throw (IOException) th;
-      if (th instanceof RuntimeException) throw (RuntimeException) th;
-      if (th instanceof Error) throw (Error) th;
-      throw new RuntimeException(th);
+    } else {
+      reThrow(th);
     }
   }
 
@@ -119,11 +115,8 @@
 
     if (priorException != null) {
       throw priorException;
-    } else if (th != null) {
-      if (th instanceof IOException) throw (IOException) th;
-      if (th instanceof RuntimeException) throw (RuntimeException) th;
-      if (th instanceof Error) throw (Error) th;
-      throw new RuntimeException(th);
+    } else {
+      reThrow(th);
     }
   }
 
@@ -153,12 +146,7 @@
       }
     }
 
-    if (th != null) {
-      if (th instanceof IOException) throw (IOException) th;
-      if (th instanceof RuntimeException) throw (RuntimeException) th;
-      if (th instanceof Error) throw (Error) th;
-      throw new RuntimeException(th);
-    }
+    reThrow(th);
   }
   
   /**
@@ -181,12 +169,7 @@
       }
     }
 
-    if (th != null) {
-      if (th instanceof IOException) throw (IOException) th;
-      if (th instanceof RuntimeException) throw (RuntimeException) th;
-      if (th instanceof Error) throw (Error) th;
-      throw new RuntimeException(th);
-    }
+    reThrow(th);
   }
 
   /**
@@ -226,7 +209,7 @@
    * @param exception this exception should get the suppressed one added
    * @param suppressed the suppressed exception
    */
-  private static final void addSuppressed(Throwable exception, Throwable suppressed) {
+  private static void addSuppressed(Throwable exception, Throwable suppressed) {
     if (exception != null && suppressed != null) {
       exception.addSuppressed(suppressed);
     }
@@ -345,4 +328,25 @@
       close(fis, fos);
     }
   }
+
+  /**
+   * Simple utilty method that takes a previously caught
+   * {@code Throwable} and rethrows either {@code
+   * IOException} or an unchecked exception.  If the
+   * argument is null then this method does nothing.
+   */
+  public static void reThrow(Throwable th) throws IOException {
+    if (th != null) {
+      if (th instanceof IOException) {
+        throw (IOException) th;
+      }
+      if (th instanceof RuntimeException) {
+        throw (RuntimeException) th;
+      }
+      if (th instanceof Error) {
+        throw (Error) th;
+      }
+      throw new RuntimeException(th);
+    }
+  }
 }
Index: lucene/facet/src/test/org/apache/lucene/facet/search/DrillDownQueryTest.java
===================================================================
--- lucene/facet/src/test/org/apache/lucene/facet/search/DrillDownQueryTest.java	(revision 1530072)
+++ lucene/facet/src/test/org/apache/lucene/facet/search/DrillDownQueryTest.java	(working copy)
@@ -66,6 +66,10 @@
   @AfterClass
   public static void afterClassDrillDownQueryTest() throws Exception {
     IOUtils.close(reader, taxo, dir, taxoDir);
+    reader = null;
+    taxo = null;
+    dir = null;
+    taxoDir = null;
   }
 
   @BeforeClass
Index: lucene/test-framework/src/java/org/apache/lucene/store/MockDirectoryWrapper.java
===================================================================
--- lucene/test-framework/src/java/org/apache/lucene/store/MockDirectoryWrapper.java	(revision 1530072)
+++ lucene/test-framework/src/java/org/apache/lucene/store/MockDirectoryWrapper.java	(working copy)
@@ -973,4 +973,9 @@
       }
     }
   }
+
+  /** Use this when throwing fake {@code uIOException},
+   *  e.g. from {@link MockDirectoryWrapper.Failure}. */
+  public static class FakeIOException extends IOException {
+  }
 }
Index: lucene/test-framework/src/java/org/apache/lucene/util/ThrottledIndexOutput.java
===================================================================
--- lucene/test-framework/src/java/org/apache/lucene/util/ThrottledIndexOutput.java	(revision 1530072)
+++ lucene/test-framework/src/java/org/apache/lucene/util/ThrottledIndexOutput.java	(working copy)
@@ -102,11 +102,13 @@
   @Override
   public void writeBytes(byte[] b, int offset, int length) throws IOException {
     final long before = System.nanoTime();
+    // TODO: sometimes, write only half the bytes, then
+    // sleep, then 2nd half, then sleep, so we sometimes
+    // interrupt having only written not all bytes
     delegate.writeBytes(b, offset, length);
     timeElapsed += System.nanoTime() - before;
     pendingBytes += length;
     sleep(getDelay(false));
-
   }
 
   protected long getDelay(boolean closing) {
Index: lucene/CHANGES.txt
===================================================================
--- lucene/CHANGES.txt	(revision 1530072)
+++ lucene/CHANGES.txt	(working copy)
@@ -106,6 +106,10 @@
 * LUCENE-5262: Fixed file handle leaks when multiple attempts to open an 
   NRT reader hit exceptions. (Shai Erera)
 
+* LUCENE-5263: Transient IOExceptions, e.g. due to disk full or file
+  descriptor exhaustion, hit at unlucky times inside IndexWriter could
+  lead to silently losing deletions. (Shai Erera, Mike McCandless)
+
 API Changes:
 
 * LUCENE-5222: Add SortField.needsScores(). Previously it was not possible