diff --git a/pregelix/pregelix-core/pom.xml b/pregelix/pregelix-core/pom.xml
index a3f24f4..b3714f7 100644
--- a/pregelix/pregelix-core/pom.xml
+++ b/pregelix/pregelix-core/pom.xml
@@ -91,14 +91,30 @@
 				<executions>
 					<execution>
 						<configuration>
+							<platforms>
+								<platform>unix</platform>
+							</platforms>
 							<programs>
 								<program>
 									<mainClass>org.apache.hadoop.util.RunJar</mainClass>
-									<name>pregelix-obselete</name>
+									<name>pregelix</name>
+								</program>
+								<program>
+									<mainClass>edu.uci.ics.hyracks.control.cc.CCDriver</mainClass>
+									<name>pregelixcc</name>
+								</program>
+								<program>
+									<mainClass>edu.uci.ics.hyracks.control.nc.NCDriver</mainClass>
+									<name>pregelixnc</name>
+									<commandLineArguments>
+										<commandLineArgument>-app-nc-main-class</commandLineArgument>
+										<commandLineArgument>edu.uci.ics.pregelix.runtime.bootstrap.NCApplicationEntryPoint</commandLineArgument>
+									</commandLineArguments>
 								</program>
 							</programs>
 							<repositoryLayout>flat</repositoryLayout>
 							<repositoryName>lib</repositoryName>
+							<configurationDirectory>etc:"$HADOOP_HOME"/conf:/etc/hadoop/conf</configurationDirectory>
 						</configuration>
 						<phase>package</phase>
 						<goals>
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelix b/pregelix/pregelix-core/src/main/resources/scripts/pregelix
deleted file mode 100644
index 7232ccc..0000000
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelix
+++ /dev/null
@@ -1,111 +0,0 @@
-#!/bin/sh
-#
-#------------------------------------------------------------------------
-# Copyright 2009-2013 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.
-# ------------------------------------------------------------------------
-#
-
-
-# resolve links - $0 may be a softlink
-PRG="$0"
-
-while [ -h "$PRG" ]; do
-  ls=`ls -ld "$PRG"`
-  link=`expr "$ls" : '.*-> \(.*\)$'`
-  if expr "$link" : '/.*' > /dev/null; then
-    PRG="$link"
-  else
-    PRG=`dirname "$PRG"`/"$link"
-  fi
-done
-
-PRGDIR=`dirname "$PRG"`
-BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
-
-
-
-# OS specific support.  $var _must_ be set to either true or false.
-cygwin=false;
-darwin=false;
-case "`uname`" in
-  CYGWIN*) cygwin=true ;;
-  Darwin*) darwin=true
-           if [ -z "$JAVA_VERSION" ] ; then
-             JAVA_VERSION="CurrentJDK"
-           else
-             echo "Using Java version: $JAVA_VERSION"
-           fi
-           if [ -z "$JAVA_HOME" ] ; then
-             JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
-           fi
-           ;;
-esac
-
-if [ -z "$JAVA_HOME" ] ; then
-  if [ -r /etc/gentoo-release ] ; then
-    JAVA_HOME=`java-config --jre-home`
-  fi
-fi
-
-# For Cygwin, ensure paths are in UNIX format before anything is touched
-if $cygwin ; then
-  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
-fi
-
-# If a specific java binary isn't specified search for the standard 'java' binary
-if [ -z "$JAVACMD" ] ; then
-  if [ -n "$JAVA_HOME"  ] ; then
-    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
-      # IBM's JDK on AIX uses strange locations for the executables
-      JAVACMD="$JAVA_HOME/jre/sh/java"
-    else
-      JAVACMD="$JAVA_HOME/bin/java"
-    fi
-  else
-    JAVACMD=`which java`
-  fi
-fi
-
-if [ ! -x "$JAVACMD" ] ; then
-  echo "Error: JAVA_HOME is not defined correctly." 1>&2
-  echo "  We cannot execute $JAVACMD" 1>&2
-  exit 1
-fi
-
-if [ -z "$REPO" ]
-then
-  REPO="$BASEDIR"/lib
-fi
-
-CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:/etc/hadoop/conf:"$BASEDIR"/etc:$1
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin; then
-  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
-  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
-  [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
-  [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
-  [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
-fi
-
-exec "$JAVACMD" $JAVA_OPTS  \
-  -classpath "$CLASSPATH" \
-  -Dapp.name="pregelix" \
-  -Dapp.pid="$$" \
-  -Dapp.repo="$REPO" \
-  -Dapp.home="$BASEDIR" \
-  -Dbasedir="$BASEDIR" \
-  org.apache.hadoop.util.RunJar \
-  "$@"
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelix.bat b/pregelix/pregelix-core/src/main/resources/scripts/pregelix.bat
deleted file mode 100644
index fe53029..0000000
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelix.bat
+++ /dev/null
@@ -1,124 +0,0 @@
-@rem /*
-@rem Copyright 2009-2013 by The Regents of the University of California
-@rem Licensed under the Apache License, Version 2.0 (the "License");
-@rem you may not use this file except in compliance with the License.
-@rem you may obtain a copy of the License from
-@rem 
-@rem     http://www.apache.org/licenses/LICENSE-2.0
-@rem 
-@rem Unless required by applicable law or agreed to in writing, software
-@rem distributed under the License is distributed on an "AS IS" BASIS,
-@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@rem See the License for the specific language governing permissions and
-@rem limitations under the License.
-@rem */
-@REM ----------------------------------------------------------------------------
-@REM  Copyright 2001-2006 The Apache Software Foundation.
-@REM
-@REM  Licensed under the Apache License, Version 2.0 (the "License");
-@REM  you may not use this file except in compliance with the License.
-@REM  You may obtain a copy of the License at
-@REM
-@REM       http://www.apache.org/licenses/LICENSE-2.0
-@REM
-@REM  Unless required by applicable law or agreed to in writing, software
-@REM  distributed under the License is distributed on an "AS IS" BASIS,
-@REM  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@REM  See the License for the specific language governing permissions and
-@REM  limitations under the License.
-@REM ----------------------------------------------------------------------------
-@REM
-@REM   Copyright (c) 2001-2006 The Apache Software Foundation.  All rights
-@REM   reserved.
-
-@echo off
-
-set ERROR_CODE=0
-
-:init
-@REM Decide how to startup depending on the version of windows
-
-@REM -- Win98ME
-if NOT "%OS%"=="Windows_NT" goto Win9xArg
-
-@REM set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" @setlocal
-
-@REM -- 4NT shell
-if "%eval[2+2]" == "4" goto 4NTArgs
-
-@REM -- Regular WinNT shell
-set CMD_LINE_ARGS=%*
-goto WinNTGetScriptDir
-
-@REM The 4NT Shell from jp software
-:4NTArgs
-set CMD_LINE_ARGS=%$
-goto WinNTGetScriptDir
-
-:Win9xArg
-@REM Slurp the command line arguments.  This loop allows for an unlimited number
-@REM of arguments (up to the command line limit, anyway).
-set CMD_LINE_ARGS=
-:Win9xApp
-if %1a==a goto Win9xGetScriptDir
-set CMD_LINE_ARGS=%CMD_LINE_ARGS% %1
-shift
-goto Win9xApp
-
-:Win9xGetScriptDir
-set SAVEDIR=%CD%
-%0\
-cd %0\..\.. 
-set BASEDIR=%CD%
-cd %SAVEDIR%
-set SAVE_DIR=
-goto repoSetup
-
-:WinNTGetScriptDir
-set BASEDIR=%~dp0\..
-
-:repoSetup
-
-
-if "%JAVACMD%"=="" set JAVACMD=java
-
-if "%REPO%"=="" set REPO=%BASEDIR%\lib
-
-cp $BASEDIR"\..\a-hadoop-patch.jar "$REPO"\
-
-set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\a-hadoop-patch.jar;"%REPO%"\pregelix-api-0.0.1-SNAPSHOT.jar;"%REPO%"\hyracks-dataflow-common-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-api-0.2.2-SNAPSHOT.jar;"%REPO%"\json-20090211.jar;"%REPO%"\httpclient-4.1-alpha2.jar;"%REPO%"\httpcore-4.1-beta1.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\commons-codec-1.3.jar;"%REPO%"\args4j-2.0.12.jar;"%REPO%"\hyracks-ipc-0.2.2-SNAPSHOT.jar;"%REPO%"\commons-lang3-3.1.jar;"%REPO%"\hyracks-data-std-0.2.2-SNAPSHOT.jar;"%REPO%"\hadoop-core-0.20.2.jar;"%REPO%"\commons-cli-1.2.jar;"%REPO%"\xmlenc-0.52.jar;"%REPO%"\commons-httpclient-3.0.1.jar;"%REPO%"\commons-net-1.4.1.jar;"%REPO%"\oro-2.0.8.jar;"%REPO%"\jetty-6.1.14.jar;"%REPO%"\jetty-util-6.1.14.jar;"%REPO%"\servlet-api-2.5-6.1.14.jar;"%REPO%"\jasper-runtime-5.5.12.jar;"%REPO%"\jasper-compiler-5.5.12.jar;"%REPO%"\jsp-api-2.1-6.1.14.jar;"%REPO%"\jsp-2.1-6.1.14.jar;"%REPO%"\core-3.1.1.jar;"%REPO%"\ant-1.6.5.jar;"%REPO%"\commons-el-1.0.jar;"%REPO%"\jets3t-0.7.1.jar;"%REPO%"\kfs-0.3.jar;"%REPO%"\hsqldb-1.8.0.10.jar;"%REPO%"\pregelix-dataflow-std-0.0.1-SNAPSHOT.jar;"%REPO%"\pregelix-dataflow-std-base-0.0.1-SNAPSHOT.jar;"%REPO%"\hyracks-dataflow-std-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-dataflow-hadoop-0.2.2-SNAPSHOT.jar;"%REPO%"\dcache-client-0.0.1.jar;"%REPO%"\jetty-client-8.0.0.M0.jar;"%REPO%"\jetty-http-8.0.0.RC0.jar;"%REPO%"\jetty-io-8.0.0.RC0.jar;"%REPO%"\jetty-util-8.0.0.RC0.jar;"%REPO%"\hyracks-storage-am-common-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-storage-common-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-storage-am-btree-0.2.2-SNAPSHOT.jar;"%REPO%"\btreehelper-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-control-cc-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-control-common-0.2.2-SNAPSHOT.jar;"%REPO%"\commons-io-1.3.1.jar;"%REPO%"\jetty-server-8.0.0.RC0.jar;"%REPO%"\servlet-api-3.0.20100224.jar;"%REPO%"\jetty-continuation-8.0.0.RC0.jar;"%REPO%"\jetty-webapp-8.0.0.RC0.jar;"%REPO%"\jetty-xml-8.0.0.RC0.jar;"%REPO%"\jetty-servlet-8.0.0.RC0.jar;"%REPO%"\jetty-security-8.0.0.RC0.jar;"%REPO%"\wicket-core-1.5.2.jar;"%REPO%"\wicket-util-1.5.2.jar;"%REPO%"\slf4j-api-1.6.1.jar;"%REPO%"\wicket-request-1.5.2.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\hyracks-control-nc-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-net-0.2.2-SNAPSHOT.jar;"%REPO%"\hyracks-hadoop-compat-0.2.2-SNAPSHOT.jar;"%REPO%"\pregelix-dataflow-0.0.1-SNAPSHOT.jar;"%REPO%"\pregelix-runtime-0.0.1-SNAPSHOT.jar;"%REPO%"\hadoop-test-0.20.2.jar;"%REPO%"\ftplet-api-1.0.0.jar;"%REPO%"\mina-core-2.0.0-M5.jar;"%REPO%"\ftpserver-core-1.0.0.jar;"%REPO%"\ftpserver-deprecated-1.0.0-M2.jar;"%REPO%"\javax.servlet-api-3.0.1.jar;"%REPO%"\pregelix-core-0.0.1-SNAPSHOT.jar
-goto endInit
-
-@REM Reaching here means variables are defined and arguments have been captured
-:endInit
-
-%JAVACMD% %JAVA_OPTS%  -classpath %CLASSPATH_PREFIX%;%CLASSPATH% -Dapp.name="pregelix" -Dapp.repo="%REPO%" -Dapp.home="%BASEDIR%" -Dbasedir="%BASEDIR%" org.apache.hadoop.util.RunJar %CMD_LINE_ARGS%
-if ERRORLEVEL 1 goto error
-goto end
-
-:error
-if "%OS%"=="Windows_NT" @endlocal
-set ERROR_CODE=%ERRORLEVEL%
-
-:end
-@REM set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" goto endNT
-
-@REM For old DOS remove the set variables from ENV - we assume they were not set
-@REM before we started - at least we don't leave any baggage around
-set CMD_LINE_ARGS=
-goto postExec
-
-:endNT
-@REM If error code is set to 1 then the endlocal was done already in :error.
-if %ERROR_CODE% EQU 0 @endlocal
-
-
-:postExec
-
-if "%FORCE_EXIT_ON_ERROR%" == "on" (
-  if %ERROR_CODE% NEQ 0 exit %ERROR_CODE%
-)
-
-exit /B %ERROR_CODE%
\ No newline at end of file
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc b/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc
deleted file mode 100755
index c1ee3f2..0000000
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelixcc
+++ /dev/null
@@ -1,114 +0,0 @@
-#!/bin/sh
-#
-#------------------------------------------------------------------------
-# Copyright 2009-2013 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.
-# ------------------------------------------------------------------------
-#
-
-# resolve links - $0 may be a softlink
-PRG="$0"
-
-while [ -h "$PRG" ]; do
-  ls=`ls -ld "$PRG"`
-  link=`expr "$ls" : '.*-> \(.*\)$'`
-  if expr "$link" : '/.*' > /dev/null; then
-    PRG="$link"
-  else
-    PRG=`dirname "$PRG"`/"$link"
-  fi
-done
-
-PRGDIR=`dirname "$PRG"`
-BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
-
-
-
-# OS specific support.  $var _must_ be set to either true or false.
-cygwin=false;
-darwin=false;
-case "`uname`" in
-  CYGWIN*) cygwin=true ;;
-  Darwin*) darwin=true
-           if [ -z "$JAVA_VERSION" ] ; then
-             JAVA_VERSION="CurrentJDK"
-           else
-             echo "Using Java version: $JAVA_VERSION"
-           fi
-           if [ -z "$JAVA_HOME" ] ; then
-             JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
-           fi
-           ;;
-esac
-
-if [ -z "$JAVA_HOME" ] ; then
-  if [ -r /etc/gentoo-release ] ; then
-    JAVA_HOME=`java-config --jre-home`
-  fi
-fi
-
-# For Cygwin, ensure paths are in UNIX format before anything is touched
-if $cygwin ; then
-  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
-fi
-
-# If a specific java binary isn't specified search for the standard 'java' binary
-if [ -z "$JAVACMD" ] ; then
-  if [ -n "$JAVA_HOME"  ] ; then
-    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
-      # IBM's JDK on AIX uses strange locations for the executables
-      JAVACMD="$JAVA_HOME/jre/sh/java"
-    else
-      JAVACMD="$JAVA_HOME/bin/java"
-    fi
-  else
-    JAVACMD=`which java`
-  fi
-fi
-
-if [ ! -x "$JAVACMD" ] ; then
-  echo "Error: JAVA_HOME is not defined correctly." 1>&2
-  echo "  We cannot execute $JAVACMD" 1>&2
-  exit 1
-fi
-
-if [ -z "$REPO" ]
-then
-  REPO="$BASEDIR"/lib
-fi
-
-CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:/etc/hadoop/conf:"$BASEDIR"/etc:$1
-
-for f in ${REPO}/*.jar; do
-  CLASSPATH=${CLASSPATH}:$f;
-done
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin; then
-  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
-  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
-  [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
-  [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
-  [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
-fi
-
-exec "$JAVACMD" $JAVA_OPTS  \
-  -classpath "$CLASSPATH" \
-  -Dapp.name="pregelixcc" \
-  -Dapp.pid="$$" \
-  -Dapp.repo="$REPO" \
-  -Dapp.home="$BASEDIR" \
-  -Dbasedir="$BASEDIR" \
-  edu.uci.ics.hyracks.control.cc.CCDriver \
-  "$@"
diff --git a/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc b/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc
deleted file mode 100755
index c01b4b4..0000000
--- a/pregelix/pregelix-core/src/main/resources/scripts/pregelixnc
+++ /dev/null
@@ -1,115 +0,0 @@
-#!/bin/sh
-#
-#------------------------------------------------------------------------
-# Copyright 2009-2013 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.
-# ------------------------------------------------------------------------
-#
-
-# resolve links - $0 may be a softlink
-PRG="$0"
-
-while [ -h "$PRG" ]; do
-  ls=`ls -ld "$PRG"`
-  link=`expr "$ls" : '.*-> \(.*\)$'`
-  if expr "$link" : '/.*' > /dev/null; then
-    PRG="$link"
-  else
-    PRG=`dirname "$PRG"`/"$link"
-  fi
-done
-
-PRGDIR=`dirname "$PRG"`
-BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
-
-
-
-# OS specific support.  $var _must_ be set to either true or false.
-cygwin=false;
-darwin=false;
-case "`uname`" in
-  CYGWIN*) cygwin=true ;;
-  Darwin*) darwin=true
-           if [ -z "$JAVA_VERSION" ] ; then
-             JAVA_VERSION="CurrentJDK"
-           else
-             echo "Using Java version: $JAVA_VERSION"
-           fi
-           if [ -z "$JAVA_HOME" ] ; then
-             JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
-           fi
-           ;;
-esac
-
-if [ -z "$JAVA_HOME" ] ; then
-  if [ -r /etc/gentoo-release ] ; then
-    JAVA_HOME=`java-config --jre-home`
-  fi
-fi
-
-# For Cygwin, ensure paths are in UNIX format before anything is touched
-if $cygwin ; then
-  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
-  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
-fi
-
-# If a specific java binary isn't specified search for the standard 'java' binary
-if [ -z "$JAVACMD" ] ; then
-  if [ -n "$JAVA_HOME"  ] ; then
-    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
-      # IBM's JDK on AIX uses strange locations for the executables
-      JAVACMD="$JAVA_HOME/jre/sh/java"
-    else
-      JAVACMD="$JAVA_HOME/bin/java"
-    fi
-  else
-    JAVACMD=`which java`
-  fi
-fi
-
-if [ ! -x "$JAVACMD" ] ; then
-  echo "Error: JAVA_HOME is not defined correctly." 1>&2
-  echo "  We cannot execute $JAVACMD" 1>&2
-  exit 1
-fi
-
-if [ -z "$REPO" ]
-then
-  REPO="$BASEDIR"/lib
-fi
-
-CLASSPATH=$CLASSPATH_PREFIX:"$HADOOP_HOME"/conf:/etc/hadoop/conf:"$BASEDIR"/etc:$1
-
-for f in ${REPO}/*.jar; do
-  CLASSPATH=${CLASSPATH}:$f;
-done
-
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin; then
-  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
-  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
-  [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`2
-  [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
-  [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
-fi
-
-exec "$JAVACMD" $JAVA_OPTS  \
-  -classpath "$CLASSPATH" \
-  -Dapp.name="pregelixnc" \
-  -Dapp.pid="$$" \
-  -Dapp.repo="$REPO" \
-  -Dapp.home="$BASEDIR" \
-  -Dbasedir="$BASEDIR" \
-  edu.uci.ics.hyracks.control.nc.NCDriver \
-  -app-nc-main-class edu.uci.ics.pregelix.runtime.bootstrap.NCApplicationEntryPoint "$@"