diff --git a/modules/elasticsearch/src/main/java/org/elasticsearch/index/engine/robin/RobinEngine.java b/modules/elasticsearch/src/main/java/org/elasticsearch/index/engine/robin/RobinEngine.java
index 0c082cef59d..263bafb11e4 100644
--- a/modules/elasticsearch/src/main/java/org/elasticsearch/index/engine/robin/RobinEngine.java
+++ b/modules/elasticsearch/src/main/java/org/elasticsearch/index/engine/robin/RobinEngine.java
@@ -116,6 +116,20 @@ public class RobinEngine extends AbstractIndexShardComponent implements Engine,
         this.mergeScheduler = mergeScheduler;
         this.analysisService = analysisService;
         this.similarityService = similarityService;
+
+        // clear the index dir by creating a new index
+        try {
+            // release locks when started
+            if (IndexWriter.isLocked(store.directory())) {
+                logger.trace("Shard is locked, releasing lock");
+                store.directory().clearLock(IndexWriter.WRITE_LOCK_NAME);
+            }
+            IndexWriter writer = new IndexWriter(store.directory(), analysisService.defaultIndexAnalyzer(), true, IndexWriter.MaxFieldLength.UNLIMITED);
+            writer.commit();
+            writer.close();
+        } catch (IOException e) {
+            logger.warn("Failed to clean the index", e);
+        }
     }
 
     @Override public void start() throws EngineException {
diff --git a/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/MmapFsStore.java b/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/MmapFsStore.java
index 5a3c3f27198..1c9ebbf7d6b 100644
--- a/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/MmapFsStore.java
+++ b/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/MmapFsStore.java
@@ -19,9 +19,7 @@
 
 package org.elasticsearch.index.store.fs;
 
-import org.apache.lucene.store.Directory;
-import org.apache.lucene.store.FSDirectory;
-import org.apache.lucene.store.MMapDirectory;
+import org.apache.lucene.store.*;
 import org.elasticsearch.env.Environment;
 import org.elasticsearch.index.LocalNodeId;
 import org.elasticsearch.index.settings.IndexSettings;
@@ -53,12 +51,19 @@ public class MmapFsStore extends AbstractFsStore<Directory> {
         super(shardId, indexSettings);
         // by default, we don't need to sync to disk, since we use the gateway
         this.syncToDisk = componentSettings.getAsBoolean("sync_to_disk", false);
-        this.fsDirectory = new CustomMMapDirectory(createStoreFilePath(environment.workWithClusterFile(), localNodeId, shardId, MAIN_INDEX_SUFFIX), syncToDisk);
+        String fsLock = componentSettings.get("use_fs_lock", "none");
+        LockFactory lockFactory = new NoLockFactory();
+        if (fsLock.equals("native")) {
+            lockFactory = new NativeFSLockFactory();
+        } else if (fsLock.equals("simple")) {
+            lockFactory = new SimpleFSLockFactory();
+        }
+        this.fsDirectory = new CustomMMapDirectory(createStoreFilePath(environment.workWithClusterFile(), localNodeId, shardId, MAIN_INDEX_SUFFIX), lockFactory, syncToDisk);
 
         SwitchDirectory switchDirectory = buildSwitchDirectoryIfNeeded(fsDirectory);
         if (switchDirectory != null) {
             suggestUseCompoundFile = false;
-            logger.debug("Using [mmap_fs] Store with path [{}], cache [true] with extensions [{}]", new Object[]{fsDirectory.getFile(), switchDirectory.primaryExtensions()});
+            logger.debug("Using [mmap_fs] Store with path [{}], cache [true] with extensions [{}]", fsDirectory.getFile(), switchDirectory.primaryExtensions());
             directory = switchDirectory;
         } else {
             suggestUseCompoundFile = true;
@@ -83,8 +88,8 @@ public class MmapFsStore extends AbstractFsStore<Directory> {
 
         private final boolean syncToDisk;
 
-        private CustomMMapDirectory(File path, boolean syncToDisk) throws IOException {
-            super(path);
+        private CustomMMapDirectory(File path, LockFactory lockFactory, boolean syncToDisk) throws IOException {
+            super(path, lockFactory);
             this.syncToDisk = syncToDisk;
         }
 
diff --git a/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/NioFsStore.java b/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/NioFsStore.java
index 2ecba6f080c..4037f7396d7 100644
--- a/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/NioFsStore.java
+++ b/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/NioFsStore.java
@@ -19,9 +19,7 @@
 
 package org.elasticsearch.index.store.fs;
 
-import org.apache.lucene.store.Directory;
-import org.apache.lucene.store.FSDirectory;
-import org.apache.lucene.store.NIOFSDirectory;
+import org.apache.lucene.store.*;
 import org.elasticsearch.env.Environment;
 import org.elasticsearch.index.LocalNodeId;
 import org.elasticsearch.index.settings.IndexSettings;
@@ -53,12 +51,19 @@ public class NioFsStore extends AbstractFsStore<Directory> {
         super(shardId, indexSettings);
         // by default, we don't need to sync to disk, since we use the gateway
         this.syncToDisk = componentSettings.getAsBoolean("sync_to_disk", false);
-        this.fsDirectory = new CustomNioFSDirectory(createStoreFilePath(environment.workWithClusterFile(), localNodeId, shardId, MAIN_INDEX_SUFFIX), syncToDisk);
+        String fsLock = componentSettings.get("use_fs_lock", "none");
+        LockFactory lockFactory = new NoLockFactory();
+        if (fsLock.equals("native")) {
+            lockFactory = new NativeFSLockFactory();
+        } else if (fsLock.equals("simple")) {
+            lockFactory = new SimpleFSLockFactory();
+        }
+        this.fsDirectory = new CustomNioFSDirectory(createStoreFilePath(environment.workWithClusterFile(), localNodeId, shardId, MAIN_INDEX_SUFFIX), lockFactory, syncToDisk);
 
         SwitchDirectory switchDirectory = buildSwitchDirectoryIfNeeded(fsDirectory);
         if (switchDirectory != null) {
             suggestUseCompoundFile = false;
-            logger.debug("Using [nio_fs] Store with path [{}], cache [true] with extensions [{}]", new Object[]{fsDirectory.getFile(), switchDirectory.primaryExtensions()});
+            logger.debug("Using [nio_fs] Store with path [{}], cache [true] with extensions [{}]", fsDirectory.getFile(), switchDirectory.primaryExtensions());
             directory = switchDirectory;
         } else {
             suggestUseCompoundFile = true;
@@ -83,8 +88,8 @@ public class NioFsStore extends AbstractFsStore<Directory> {
 
         private final boolean syncToDisk;
 
-        private CustomNioFSDirectory(File path, boolean syncToDisk) throws IOException {
-            super(path);
+        private CustomNioFSDirectory(File path, LockFactory lockFactory, boolean syncToDisk) throws IOException {
+            super(path, lockFactory);
             this.syncToDisk = syncToDisk;
         }
 
diff --git a/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/SimpleFsStore.java b/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/SimpleFsStore.java
index 2f0a5e3d346..cf9735b88c1 100644
--- a/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/SimpleFsStore.java
+++ b/modules/elasticsearch/src/main/java/org/elasticsearch/index/store/fs/SimpleFsStore.java
@@ -19,9 +19,7 @@
 
 package org.elasticsearch.index.store.fs;
 
-import org.apache.lucene.store.Directory;
-import org.apache.lucene.store.FSDirectory;
-import org.apache.lucene.store.SimpleFSDirectory;
+import org.apache.lucene.store.*;
 import org.elasticsearch.env.Environment;
 import org.elasticsearch.index.LocalNodeId;
 import org.elasticsearch.index.settings.IndexSettings;
@@ -53,12 +51,19 @@ public class SimpleFsStore extends AbstractFsStore<Directory> {
         super(shardId, indexSettings);
         // by default, we don't need to sync to disk, since we use the gateway
         this.syncToDisk = componentSettings.getAsBoolean("sync_to_disk", false);
-        this.fsDirectory = new CustomSimpleFSDirectory(createStoreFilePath(environment.workWithClusterFile(), localNodeId, shardId, MAIN_INDEX_SUFFIX), syncToDisk);
+        String fsLock = componentSettings.get("use_fs_lock", "none");
+        LockFactory lockFactory = new NoLockFactory();
+        if (fsLock.equals("native")) {
+            lockFactory = new NativeFSLockFactory();
+        } else if (fsLock.equals("simple")) {
+            lockFactory = new SimpleFSLockFactory();
+        }
+        this.fsDirectory = new CustomSimpleFSDirectory(createStoreFilePath(environment.workWithClusterFile(), localNodeId, shardId, MAIN_INDEX_SUFFIX), lockFactory, syncToDisk);
 
         SwitchDirectory switchDirectory = buildSwitchDirectoryIfNeeded(fsDirectory);
         if (switchDirectory != null) {
             suggestUseCompoundFile = false;
-            logger.debug("Using [simple_fs] Store with path [{}], cache [true] with extensions [{}]", new Object[]{fsDirectory.getFile(), switchDirectory.primaryExtensions()});
+            logger.debug("Using [simple_fs] Store with path [{}], cache [true] with extensions [{}]", fsDirectory.getFile(), switchDirectory.primaryExtensions());
             directory = switchDirectory;
         } else {
             suggestUseCompoundFile = true;
@@ -83,8 +88,8 @@ public class SimpleFsStore extends AbstractFsStore<Directory> {
 
         private final boolean syncToDisk;
 
-        private CustomSimpleFSDirectory(File path, boolean syncToDisk) throws IOException {
-            super(path);
+        private CustomSimpleFSDirectory(File path, LockFactory lockFactory, boolean syncToDisk) throws IOException {
+            super(path, lockFactory);
             this.syncToDisk = syncToDisk;
         }
 
diff --git a/modules/elasticsearch/src/test/java/org/elasticsearch/index/engine/AbstractSimpleEngineTests.java b/modules/elasticsearch/src/test/java/org/elasticsearch/index/engine/AbstractSimpleEngineTests.java
index 63e42eb16d0..b97dfcde62c 100644
--- a/modules/elasticsearch/src/test/java/org/elasticsearch/index/engine/AbstractSimpleEngineTests.java
+++ b/modules/elasticsearch/src/test/java/org/elasticsearch/index/engine/AbstractSimpleEngineTests.java
@@ -212,18 +212,6 @@ public abstract class AbstractSimpleEngineTests {
         searchResult.release();
 
         engine.close();
-
-        // TODO check that operations on engine will throw an EngineAlreadyClosed exception (and while you are at it, create the exception as well)
-
-        // now create a new engine, it should see the flushed changes
-        engine = createEngine(store);
-        engine.start();
-
-        searchResult = engine.searcher();
-        assertThat(searchResult, engineSearcherTotalHits(1));
-        assertThat(searchResult, engineSearcherTotalHits(new TermQuery(new Term("value", "test")), 0));
-        assertThat(searchResult, engineSearcherTotalHits(new TermQuery(new Term("value", "test1")), 1));
-        searchResult.release();
     }
 
     @Test public void testSearchResultRelease() throws Exception {