diff --git a/pregelix/pregelix-runtime/pom.xml b/pregelix/pregelix-runtime/pom.xml
index bce7b12..29b6ba7 100644
--- a/pregelix/pregelix-runtime/pom.xml
+++ b/pregelix/pregelix-runtime/pom.xml
@@ -42,8 +42,9 @@
 				</configuration>
 			</plugin>
 			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-clean-plugin</artifactId>
-				<version>2.5</version>
+				<version>2.4.1</version>
 				<configuration>
 					<filesets>
 						<fileset>
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/IndexLifeCycleManagerProvider.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/IndexLifeCycleManagerProvider.java
new file mode 100644
index 0000000..4fce6b3
--- /dev/null
+++ b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/IndexLifeCycleManagerProvider.java
@@ -0,0 +1,22 @@
+package edu.uci.ics.pregelix.runtime.bootstrap;
+
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.storage.am.common.api.IIndexLifecycleManager;
+import edu.uci.ics.hyracks.storage.am.common.api.IIndexLifecycleManagerProvider;
+import edu.uci.ics.pregelix.dataflow.context.RuntimeContext;
+
+public class IndexLifeCycleManagerProvider implements IIndexLifecycleManagerProvider {
+
+    private static final long serialVersionUID = 1L;
+
+    public static final IIndexLifecycleManagerProvider INSTANCE = new IndexLifeCycleManagerProvider();
+
+    private IndexLifeCycleManagerProvider() {
+    }
+
+    @Override
+    public IIndexLifecycleManager getLifecycleManager(IHyracksTaskContext ctx) {
+        return RuntimeContext.get(ctx).getIndexLifecycleManager();
+    }
+
+}
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/NCApplicationEntryPoint.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/NCApplicationEntryPoint.java
new file mode 100644
index 0000000..fbebc66
--- /dev/null
+++ b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/NCApplicationEntryPoint.java
@@ -0,0 +1,23 @@
+package edu.uci.ics.pregelix.runtime.bootstrap;
+
+import edu.uci.ics.hyracks.api.application.INCApplicationContext;
+import edu.uci.ics.hyracks.api.application.INCApplicationEntryPoint;
+import edu.uci.ics.pregelix.dataflow.context.RuntimeContext;
+
+public class NCApplicationEntryPoint implements INCApplicationEntryPoint {
+    @Override
+    public void start(INCApplicationContext ncAppCtx, String[] args) throws Exception {
+        RuntimeContext rCtx = new RuntimeContext(ncAppCtx);
+        ncAppCtx.setApplicationObject(rCtx);
+    }
+
+    @Override
+    public void notifyStartupComplete() throws Exception {
+
+    }
+
+    @Override
+    public void stop() throws Exception {
+
+    }
+}
\ No newline at end of file
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/NCBootstrapImpl.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/NCBootstrapImpl.java
deleted file mode 100644
index 76c725e..0000000
--- a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/NCBootstrapImpl.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2009-2010 by The Regents of the University of California
- * Licensed 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 from
- * 
- *     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.
- */
-package edu.uci.ics.pregelix.runtime.bootstrap;
-
-import java.util.logging.Logger;
-
-import edu.uci.ics.hyracks.api.application.INCApplicationContext;
-import edu.uci.ics.hyracks.api.application.INCBootstrap;
-import edu.uci.ics.pregelix.dataflow.context.RuntimeContext;
-
-public class NCBootstrapImpl implements INCBootstrap {
-    private static final Logger LOGGER = Logger.getLogger(NCBootstrapImpl.class.getName());
-    private INCApplicationContext appCtx;
-
-    @Override
-    public void start() throws Exception {
-        LOGGER.info("Starting NC Bootstrap");
-        RuntimeContext rCtx = new RuntimeContext(appCtx);
-        appCtx.setApplicationObject(rCtx);
-        LOGGER.info("Initialized RuntimeContext: " + rCtx);
-    }
-
-    @Override
-    public void stop() throws Exception {
-        LOGGER.info("Stopping NC Bootstrap");
-        RuntimeContext rCtx = (RuntimeContext) appCtx.getApplicationObject();
-        rCtx.close();
-    }
-
-    @Override
-    public void setApplicationContext(INCApplicationContext appCtx) {
-        this.appCtx = appCtx;
-    }
-}
\ No newline at end of file
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/StorageManagerInterface.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/StorageManagerInterface.java
index 57bbfbe..0cce59d 100644
--- a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/StorageManagerInterface.java
+++ b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/StorageManagerInterface.java
@@ -18,6 +18,8 @@
 import edu.uci.ics.hyracks.storage.common.IStorageManagerInterface;
 import edu.uci.ics.hyracks.storage.common.buffercache.IBufferCache;
 import edu.uci.ics.hyracks.storage.common.file.IFileMapProvider;
+import edu.uci.ics.hyracks.storage.common.file.ILocalResourceRepository;
+import edu.uci.ics.hyracks.storage.common.file.ResourceIdFactory;
 import edu.uci.ics.pregelix.dataflow.context.RuntimeContext;
 
 public class StorageManagerInterface implements IStorageManagerInterface {
@@ -37,4 +39,14 @@
     public IFileMapProvider getFileMapProvider(IHyracksTaskContext ctx) {
         return RuntimeContext.get(ctx).getFileMapManager();
     }
+
+    @Override
+    public ILocalResourceRepository getLocalResourceRepository(IHyracksTaskContext ctx) {
+        return RuntimeContext.get(ctx).getLocalResourceRepository();
+    }
+
+    @Override
+    public ResourceIdFactory getResourceIdFactory(IHyracksTaskContext ctx) {
+        return RuntimeContext.get(ctx).getResourceIdFactory();
+    }
 }
\ No newline at end of file
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/TreeIndexRegistryProvider.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/TreeIndexRegistryProvider.java
deleted file mode 100644
index 7d66422..0000000
--- a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/bootstrap/TreeIndexRegistryProvider.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2009-2010 by The Regents of the University of California
- * Licensed 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 from
- * 
- *     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.
- */
-package edu.uci.ics.pregelix.runtime.bootstrap;
-
-import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
-import edu.uci.ics.hyracks.storage.am.common.dataflow.IIndex;
-import edu.uci.ics.hyracks.storage.am.common.dataflow.IIndexRegistryProvider;
-import edu.uci.ics.hyracks.storage.am.common.dataflow.IndexRegistry;
-import edu.uci.ics.pregelix.dataflow.context.RuntimeContext;
-
-public class TreeIndexRegistryProvider implements IIndexRegistryProvider<IIndex> {
-    private static final long serialVersionUID = 1L;
-
-    public static final TreeIndexRegistryProvider INSTANCE = new TreeIndexRegistryProvider();
-
-    private TreeIndexRegistryProvider() {
-    }
-
-    @Override
-    public IndexRegistry<IIndex> getRegistry(IHyracksTaskContext ctx) {
-        return RuntimeContext.get(ctx).getTreeIndexRegistry();
-    }
-}
\ No newline at end of file
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/ComputeUpdateFunctionFactory.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/ComputeUpdateFunctionFactory.java
index f7958d9..0c09757 100644
--- a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/ComputeUpdateFunctionFactory.java
+++ b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/ComputeUpdateFunctionFactory.java
@@ -175,8 +175,12 @@
                 ArrayListWritable msgContentList = (ArrayListWritable) tuple[1];
                 msgContentList.reset(msgIterator);
 
-                if (!msgIterator.hasNext() && vertex.isHalted())
+                if (!msgIterator.hasNext() && vertex.isHalted()) {
                     return;
+                }
+                if (vertex.isHalted()) {
+                    vertex.activate();
+                }
 
                 try {
                     vertex.compute(msgIterator);
diff --git a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/StartComputeUpdateFunctionFactory.java b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/StartComputeUpdateFunctionFactory.java
index 0cf64a0..1bf6a2b 100644
--- a/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/StartComputeUpdateFunctionFactory.java
+++ b/pregelix/pregelix-runtime/src/main/java/edu/uci/ics/pregelix/runtime/function/StartComputeUpdateFunctionFactory.java
@@ -176,8 +176,12 @@
                 vertex.setOutputAppenders(appenders);
                 vertex.setOutputTupleBuilders(tbs);
 
-                if (!msgIterator.hasNext() && vertex.isHalted())
+                if (!msgIterator.hasNext() && vertex.isHalted()) {
                     return;
+                }
+                if (vertex.isHalted()) {
+                    vertex.activate();
+                }
 
                 try {
                     vertex.compute(msgIterator);