fix a few nocommits

lucene/core/src/java/org/apache/lucene/index/IndexFileDeleter.java

@@ -699,7 +699,32 @@ final class IndexFileDeleter implements Closeable {
       infoStream.message("IFD", "delete \"" + names + "\"");
     }
 
+    // We make two passes, first deleting any segments_N files, second deleting all the rest.  We do this so that if we throw exc or JVM
+    // crashes during deletions, we don't leave the index in an "apparently corrupt" state:
     for(String name : names) {
+      if (name.startsWith(IndexFileNames.SEGMENTS) == false) {
+        continue;
+      }
+      try {
+        directory.deleteFile(name);
+      } catch (NoSuchFileException | FileNotFoundException e) {
+        // IndexWriter should only ask us to delete files it knows it wrote, so if we hit this, something is wrong!
+
+        if (Constants.WINDOWS) {
+          // TODO: can we remove this OS-specific hacky logic?  If windows deleteFile is buggy, we should instead contain this workaround in
+          // a WindowsFSDirectory ...
+          // LUCENE-6684: we suppress this assert for Windows, since a file could be in a confusing "pending delete" state, and falsely
+          // return NSFE/FNFE
+        } else {
+          throw e;
+        }
+      }
+    }
+
+    for(String name : names) {
+      if (name.startsWith(IndexFileNames.SEGMENTS) == true) {
+        continue;
+      }
       try {
         directory.deleteFile(name);
       } catch (NoSuchFileException | FileNotFoundException e) {

lucene/replicator/src/java/org/apache/lucene/replicator/nrt/ReplicaFileDeleter.java

@@ -122,6 +122,7 @@ class ReplicaFileDeleter {
       node.message("file " + fileName + ": delete failed: " + missing);
       throw new IllegalStateException("file " + fileName + ": we attempted delete but the file does not exist?", missing);
     } catch (IOException ioe) {
+      // nocommit remove this retry logic!  it's Directory's job now...
       if (Node.VERBOSE_FILES) {
         node.message("file " + fileName + ": delete failed: " + ioe + "; will retry later");
       }

lucene/replicator/src/java/org/apache/lucene/replicator/nrt/ReplicaNode.java

@@ -92,8 +92,6 @@ abstract class ReplicaNode extends Node {
       // Obtain a write lock on this index since we "act like" an IndexWriter, to prevent any other IndexWriter or ReplicaNode from using it:
       writeFileLock = dir.obtainLock(IndexWriter.WRITE_LOCK_NAME);
       
-      // nocommit must check for no pending deletes here, like IW does
-
       state = "init";
       deleter = new ReplicaFileDeleter(this, dir);
     } catch (Throwable t) {

lucene/replicator/src/test/org/apache/lucene/replicator/nrt/Jobs.java

@@ -84,6 +84,7 @@ class Jobs extends Thread implements Closeable {
           topJob.onceDone.run(topJob);
         } catch (Throwable t2) {
           node.message("ignore exception calling OnceDone: " + t2);
+          t2.printStackTrace(System.out);
         }
         continue;
       }

lucene/replicator/src/test/org/apache/lucene/replicator/nrt/SimpleReplicaNode.java

@@ -135,9 +135,9 @@ class SimpleReplicaNode extends ReplicaNode {
     MockDirectoryWrapper dir = LuceneTestCase.newMockFSDirectory(path);
     
     dir.setAssertNoUnrefencedFilesOnClose(true);
-    if (doCheckIndexOnClose) {
-      dir.setCheckIndexOnClose(false);
-    }
+    // nocommit
+    //dir.setCheckIndexOnClose(doCheckIndexOnClose);
+    dir.setCheckIndexOnClose(true);
 
     // Corrupt any index files not referenced by current commit point; this is important (increases test evilness) because we may have done
     // a hard crash of the previous JVM writing to this directory and so MDW's corrupt-unknown-files-on-close never ran:

lucene/replicator/src/test/org/apache/lucene/replicator/nrt/TestNRTReplication.java

@@ -39,8 +39,6 @@ import org.apache.lucene.util.TestUtil;
 
 import com.carrotsearch.randomizedtesting.SeedUtils;
 
-// nocommit make some explicit failure tests
-
 // MockRandom's .sd file has no index header/footer:
 @SuppressCodecs({"MockRandom", "Memory", "Direct", "SimpleText"})
 @SuppressSysoutChecks(bugUrl = "Stuff gets printed, important stuff for debugging a failure")

lucene/replicator/src/test/org/apache/lucene/replicator/nrt/TestStressNRTReplication.java

@@ -161,7 +161,8 @@ public class TestStressNRTReplication extends LuceneTestCase {
   static final boolean DO_BIT_FLIPS_DURING_COPY = true;
 
   /** Set to a non-null value to force exactly that many nodes; else, it's random. */
-  static final Integer NUM_NODES = null;
+  // nocommit
+  static final Integer NUM_NODES = 2;
 
   final AtomicBoolean failed = new AtomicBoolean();
 
@@ -980,10 +981,10 @@ public class TestStressNRTReplication extends LuceneTestCase {
             continue;
           }
 
-          // nocommit not anymore?
-          // This can be null if we got the new primary after crash and that primary is still catching up (replaying xlog):
+          // This can be null if primary is flushing, has already refreshed its searcher, but is e.g. still notifying replicas and hasn't
+          // yet returned the version to us, in which case this searcher thread can see the version before the main thread has added it to
+          // versionToMarker:
           Integer expectedAtLeastHitCount = versionToMarker.get(version);
-          assertNotNull("version=" + version, expectedAtLeastHitCount);
 
           if (expectedAtLeastHitCount != null && expectedAtLeastHitCount > 0 && random().nextInt(10) == 7) {
             try {

lucene/test-framework/src/java/org/apache/lucene/store/MockDirectoryWrapper.java

@@ -230,10 +230,6 @@ public class MockDirectoryWrapper extends BaseDirectoryWrapper {
       throw (AssertionError) fillOpenTrace(new AssertionError("MockDirectoryWrapper: dest file \"" + dest + "\" is still open: cannot rename"), dest, true);
     }
 
-    if (createdFiles.contains(dest)) {
-      throw new IOException("MockDirectoryWrapper: dest file \"" + dest + "\" already exists: cannot rename");
-    }
-
     boolean success = false;
     try {
       in.renameFile(source, dest);
@@ -275,7 +271,14 @@ public class MockDirectoryWrapper extends BaseDirectoryWrapper {
     for(String fileName : listAll()) {
       if (fileName.startsWith(IndexFileNames.SEGMENTS)) {
         System.out.println("MDW: read " + fileName + " to gather files it references");
-        knownFiles.addAll(SegmentInfos.readCommit(this, fileName).files(true));
+        SegmentInfos infos;
+        try {
+          infos = SegmentInfos.readCommit(this, fileName);
+        } catch (IOException ioe) {
+          System.out.println("MDW: exception reading segment infos " + fileName + "; files: " + Arrays.toString(listAll()));
+          throw ioe;
+        }
+        knownFiles.addAll(infos.files(true));
       }
     }
 
@@ -438,7 +441,6 @@ public class MockDirectoryWrapper extends BaseDirectoryWrapper {
   /** Simulates a crash of OS or machine by overwriting
    *  unsynced files. */
   public synchronized void crash() throws IOException {
-    crashed = true;
     openFiles = new HashMap<>();
     openFilesForWrite = new HashSet<>();
     openFilesDeleted = new HashSet<>();
@@ -451,6 +453,7 @@ public class MockDirectoryWrapper extends BaseDirectoryWrapper {
       } catch (Exception ignored) {}
     }
     corruptFiles(unSyncedFiles);
+    crashed = true;
     unSyncedFiles = new HashSet<>();
   }
 
@@ -569,6 +572,7 @@ public class MockDirectoryWrapper extends BaseDirectoryWrapper {
 
     unSyncedFiles.remove(name);
     in.deleteFile(name);
+    createdFiles.remove(name);
   }
 
   // sets the cause of the incoming ioe to be the stack
@@ -846,6 +850,7 @@ public class MockDirectoryWrapper extends BaseDirectoryWrapper {
           TestUtil.checkIndex(this, getCrossCheckTermVectorsOnClose(), true);
           
           // TODO: factor this out / share w/ TestIW.assertNoUnreferencedFiles
+          // nocommit pull this outside of "getCheckIndexOnClose"
           if (assertNoUnreferencedFilesOnClose) {
 
             // now look for unreferenced files: discount ones that we tried to delete but could not