diff --git a/bin/gobblin-mapreduce.sh b/bin/gobblin-mapreduce.sh
old mode 100644
new mode 100755
index 055aee2ad56..efad5346c9f
--- a/bin/gobblin-mapreduce.sh
+++ b/bin/gobblin-mapreduce.sh
@@ -4,36 +4,129 @@
 ############### Run Gobblin Jobs on Hadoop MR ################
 ##############################################################
 
-USAGE="gobblin-mapreduce.sh <job tracker URL> <file system URL> <job configuration file>"
+FWDIR="$(cd `dirname $0`/..; pwd)"
+FWDIR_LIB=$FWDIR/lib
+FWDIR_CONF=$FWDIR/conf
+
+function print_usage(){
+  echo "Usage: gobblin-mapreduce.sh [OPTION] --conf <job configuration file>"
+  echo "Where OPTION can be:"
+  echo "  --jt <job tracker / resource manager URL>      Job submission URL: if not set, taken from \${HADOOP_HOME}/conf"
+  echo "  --fs <file system URL>                         Target file system: if not set, taken from \${HADOOP_HOME}/conf"
+  echo "  --jars <comma-separated list of job jars>      Job jar(s): if not set, "$FWDIR_LIB" is examined"
+  echo "  --workdir <job work dir>                       Gobblin's base work directory: if not set, taken from \${GOBBLIN_WORK_DIR}"
+  echo "  --help                                         Display this help and exit"
+}
+
+# Print an error message and exit
+function die() {
+  echo -e "\nError: $@\n" 1>&2
+  print_usage
+  exit 1
+}
+
+for i in "$@"
+do
+  case "$1" in
+    --jt)
+      JOB_TRACKER_URL="$2"
+      shift
+      ;;
+    --fs)
+      FS_URL="$2"
+      shift
+      ;;
+    --workdir)
+      WORK_DIR="$2"
+      shift
+      ;;
+    --jars)
+      JARS="$2"
+      shift
+      ;;
+    --conf)
+      JOB_CONFIG_FILE="$2"
+      shift
+      ;;
+    --help)
+      print_usage
+      exit 0
+      ;;
+    *)
+      ;;
+  esac
+  shift
+done
 
-if [ "$#" -ne 3 ]; then
-    echo "Usage:"
-    echo $USAGE
-    exit 1
+if [ -z "$JOB_CONFIG_FILE" ]; then 
+  die "No job configuration file set!"
 fi
 
-JOB_TRACKER_URL=$1
-FS_URL=$2
-JOB_CONFIG_FILE=$3
+# User defined work directory overrides $GOBBLIN_WORK_DIR
+if [ -n "$WORK_DIR" ]; then 
+  export GOBBLIN_WORK_DIR="$WORK_DIR"
+fi
 
-FWDIR="$(cd `dirname $0`/..; pwd)"
+if [ -z "$GOBBLIN_WORK_DIR" ]; then 
+  die "GOBBLIN_WORK_DIR is not set!"
+fi
+
+. $FWDIR_CONF/gobblin-env.sh
+
+USER_JARS=""
+separator=''
+set_user_jars(){
+  if [ -n "$1" ]; then 
+    IFS=','
+    read -ra userjars <<< "$1"
+    for userjar in ${userjars[@]}; do
+      add_user_jar "$userjar"
+     done
+    unset IFS
+  fi
+}
+
+add_user_jar(){
+  local dirname=`dirname "$1"`
+  local jarname=`basename "$1"`
+  dirname=`cd "$dirname">/dev/null; pwd`
+  USER_JARS+="$separator$dirname/$jarname"
+  separator=','
+}
+
+# Add the absoulte path of the user defined job jars to the LIBJARS first
+set_user_jars "$JARS"
 
 # Jars Gobblin runtime depends on
-LIBJARS=$FWDIR/lib/common-api.jar,$FWDIR/lib/metastore.jar,$FWDIR/lib/qualitychecker.jar,\
-$FWDIR/lib/source.jar,$FWDIR/lib/converter.jar,$FWDIR/lib/writer.jar,$FWDIR/lib/utility.jar,\
-$FWDIR/lib/guava-15.0.jar,$FWDIR/lib/avro-1.7.1.jar,$FWDIR/lib/avro-mapred-1.7.6.jar,\
-$FWDIR/lib/metrics-core-3.0.2.jar,$FWDIR/lib/gson-2.2.4.jar
+LIBJARS=$USER_JARS$separator$FWDIR_LIB/gobblin-metastore.jar,$FWDIR_LIB/gobblin-metrics.jar,\
+$FWDIR_LIB/gobblin-core.jar,$FWDIR_LIB/gobblin-api.jar,$FWDIR_LIB/gobblin-utility.jar,\
+$FWDIR_LIB/guava-15.0.jar,$FWDIR_LIB/avro-1.7.6.jar,$FWDIR_LIB/avro-mapred-1.7.6.jar,\
+$FWDIR_LIB/metrics-core-3.0.2.jar,$FWDIR_LIB/gson-2.2.4.jar,$FWDIR_LIB/joda-time-1.6.jar,$FWDIR_LIB/data-1.15.9.jar
+
+# Add libraries to the Hadoop classpath
+GOBBLIN_DEP_JARS=`echo "$USER_JARS" | tr ',' ':' `
+for jarFile in `ls $FWDIR_LIB/*`
+do
+  GOBBLIN_DEP_JARS=${GOBBLIN_DEP_JARS}:$jarFile
+done
+
+# Honor Gobblin dependencies
+export HADOOP_USER_CLASSPATH_FIRST=true
+export HADOOP_CLASSPATH=$GOBBLIN_DEP_JARS:$HADOOP_CLASSPATH
 
-export HADOOP_CLASSPATH=$FWDIR/lib/*
+GOBBLIN_CONFIG_FILE=$FWDIR_CONF/gobblin-mapreduce.properties
 
-GOBBLIN_CONFIG_FILE=$FWDIR/conf/gobblin-mapreduce.properties
+JT_COMMAND=$([ -z $JOB_TRACKER_URL ] && echo "" || echo "-jt $JOB_TRACKER_URL")
+FS_COMMAND=$([ -z $FS_URL ] && echo "" || echo "-fs $FS_URL")
 
 # Launch the job to run on Hadoop
 $HADOOP_BIN_DIR/hadoop jar \
-        $FWDIR/lib/runtime.jar \
+        $FWDIR_LIB/gobblin-runtime.jar \
         gobblin.runtime.mapreduce.CliMRJobLauncher \
-        -jt $JOB_TRACKER_URL \
-        -fs $FS_URL \
+        -D mapreduce.user.classpath.first=true \
+        -D mapreduce.job.user.classpath.first=true \
+        $JT_COMMAND \
+        $FS_COMMAND \
         -libjars $LIBJARS \
-        $GOBBLIN_CONFIG_FILE \
-        $JOB_CONFIG_FILE
+        -sysconfig $GOBBLIN_CONFIG_FILE \
+        -jobconfig $JOB_CONFIG_FILE
\ No newline at end of file
diff --git a/bin/gobblin-standalone.sh b/bin/gobblin-standalone.sh
index 9fe29f88d11..f47111ba498 100755
--- a/bin/gobblin-standalone.sh
+++ b/bin/gobblin-standalone.sh
@@ -1,30 +1,87 @@
 #!/bin/bash
 
-USAGE="gobblin-standalone.sh <start | status | restart | stop>"
+FWDIR="$(cd `dirname $0`/..; pwd)"
+FWDIR_LIB=$FWDIR/lib
+FWDIR_CONF=$FWDIR/conf
+
+function print_usage(){
+  echo "gobblin-standalone.sh <start | status | restart | stop> [OPTION]"
+  echo "Where:"
+  echo "  --workdir <job work dir>                       Gobblin's base work directory: if not set, taken from \${GOBBLIN_WORK_DIR}"
+  echo "  --jars <comma-separated list of job jars>      Job jar(s): if not set, "$FWDIR_LIB" is examined"
+  echo "  --conf <directory of job configuration files>  Directory of job configuration files: if not set, taken from ${GOBBLIN_JOB_CONFIG_DIR}"
+  echo "  --help                                         Display this help and exit"
+}
 
-if [ "$#" -ne 1 ]; then
-  echo "Usage:"
-  echo $USAGE
+# Print an error message and exit
+function die() {
+  echo -e "\nError: $@\n" 1>&2
+  print_usage
   exit 1
+}
+
+for i in "$@"
+do
+  case "$1" in
+    start|stop|restart|status)
+      ACTION="$1"
+      ;;
+    --workdir)
+      WORK_DIR="$2"
+      shift
+      ;;
+    --jars)
+      JARS="$2"
+      shift
+      ;;
+    --conf)
+      JOB_CONFIG_DIR="$2"
+      shift
+      ;;
+    --help)
+      print_usage
+      exit 0
+      ;;
+    *)
+      ;;
+  esac
+  shift
+done
+
+if [ -z "$JAVA_HOME" ]; then
+  die "Environment variable JAVA_HOME not set!"
+fi
+
+check=false
+if [ $ACTION == "start" ] || [ $ACTION == "restart" ]; then 
+  check=true
 fi
 
-if [ -z $GOBBLIN_WORK_DIR ]; then
-  echo "Environment variable GOBBLIN_WORK_DIR not set"
+# User defined job configuration directory overrides $GOBBLIN_JOB_CONFIG_DIR
+if [ -n "$JOB_CONFIG_DIR" ]; then 
+  export GOBBLIN_JOB_CONFIG_DIR="$JOB_CONFIG_DIR"
 fi
 
-if [ -z $JAVA_HOME ]; then
-  echo "Environment variable JAVA_HOME not set"
+if [ -z "$GOBBLIN_JOB_CONFIG_DIR" ] && [ "$check" == true ]; then
+  die "Environment variable GOBBLIN_JOB_CONFIG_DIR not set!"
 fi
 
-ACTION=$1
+# User defined work directory overrides $GOBBLIN_WORK_DIR
+if [ -n "$WORK_DIR" ]; then 
+  export GOBBLIN_WORK_DIR="$WORK_DIR"
+fi
 
-FWDIR="$(cd `dirname $0`/..; pwd)"
+if [ -z "$GOBBLIN_WORK_DIR" ] && [ "$check" == true ]; then 
+  die "GOBBLIN_WORK_DIR is not set!"
+fi
+
+. $FWDIR_CONF/gobblin-env.sh
 
-CONFIG_FILE=$FWDIR/conf/gobblin-standalone.properties
+CONFIG_FILE=$FWDIR_CONF/gobblin-standalone.properties
 
 PID="$GOBBLIN_WORK_DIR/.gobblin-pid"
 
-if [ -f $PID ]; then
+if [ -f "$PID" ]; then
   PID_VALUE=`cat $PID` > /dev/null 2>&1
 else
   PID_VALUE=""
@@ -34,22 +91,39 @@ if [ ! -d "$FWDIR/logs" ]; then
   mkdir "$FWDIR/logs"
 fi
 
+set_user_jars(){
+  local separator=''
+  if [ -n "$1" ]; then 
+    IFS=','
+    read -ra userjars <<< "$1"
+    for userjar in ${userjars[@]}; do
+      add_user_jar "$userjar"
+     done
+    unset IFS
+  fi
+}
+
+add_user_jar(){
+  local dirname=`dirname "$1"`
+  local jarname=`basename "$1"`
+  dirname=`cd "$dirname">/dev/null; pwd`
+  GOBBLIN_JARS+="$separator$dirname/$jarname"
+  separator=':'
+}
+
+# Add the absoulte path of the user defined job jars to the GOBBLIN_JARS
+set_user_jars "$JARS"
+
 start() {
-  GOBBLIN_JARS=""
-  for jar in $(ls -d $FWDIR/lib/*); do
+  for jar in $(ls -d $FWDIR_LIB/*); do
     if [ "$GOBBLIN_JARS" != "" ]; then
       GOBBLIN_JARS+=":$jar"
     else
       GOBBLIN_JARS=$jar
     fi
   done
-
-  if [ -z $GOBBLIN_JOB_JARS ]; then
-    CLASSPATH=$GOBBLIN_JARS
-  else
-    CLASSPATH=$GOBBLIN_JARS:$GOBBLIN_JOB_JARS
-  fi
-  CLASSPATH+=":$FWDIR/conf"
+  
+  CLASSPATH="$GOBBLIN_JARS:$FWDIR_CONF"
 
   echo "Starting Gobblin standalone daemon"
   COMMAND="$JAVA_HOME/bin/java -Xmx2g -Xms1g "
@@ -59,9 +133,9 @@ start() {
   COMMAND+="-XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=$FWDIR/logs/ "
   COMMAND+="-Xloggc:$FWDIR/logs/gobblin-gc.log "
   COMMAND+="-Dgobblin.logs.dir=$FWDIR/logs "
-  COMMAND+="-Dlog4j.configuration=file://$FWDIR/conf/log4j-standalone.xml "
+  COMMAND+="-Dlog4j.configuration=file://$FWDIR_CONF/log4j-standalone.xml "
   COMMAND+="-cp $CLASSPATH "
-  COMMAND+="-Dorg.quartz.properties=$FWDIR/conf/quartz.properties "
+  COMMAND+="-Dorg.quartz.properties=$FWDIR_CONF/quartz.properties "
   COMMAND+="gobblin.scheduler.SchedulerDaemon $CONFIG_FILE"
   echo "Running command:"
   echo "$COMMAND"
@@ -69,7 +143,7 @@ start() {
 }
 
 stop() {
-  if [ -f $PID ]; then
+  if [ -f "$PID" ]; then
     if kill -0 $PID_VALUE > /dev/null 2>&1; then
       echo 'Stopping Gobblin standalone daemon'
       kill $PID_VALUE
@@ -88,7 +162,7 @@ stop() {
 
 # Check the status of the process
 status() {
-  if [ -f $PID ]; then
+  if [ -f "$PID" ]; then
     echo "Looking into file: $PID"
     if kill -0 $PID_VALUE > /dev/null 2>&1; then
       echo "Gobblin standalone daemon is running with status: "
@@ -101,7 +175,7 @@ status() {
   fi
 }
 
-case $ACTION in
+case "$ACTION" in
   "start")
     start
     ;;
diff --git a/build.gradle b/build.gradle
index 503d01ea850..cd4cff8d848 100644
--- a/build.gradle
+++ b/build.gradle
@@ -41,7 +41,7 @@ if (!project.hasProperty('pegasusVersion')) {
 
 ext.externalDependency = [
   "antlrRuntime": "org.antlr:antlr-runtime:3.0.1",
-  "avro": "org.apache.avro:avro:1.7.1",
+  "avro": "org.apache.avro:avro:1.7.6",
   "avroMapred": "org.apache.avro:avro-mapred:1.7.6",
   "commonsCli": "commons-cli:commons-cli:1.2",
   "commonsDbcp": "commons-dbcp:commons-dbcp:1.4",
@@ -135,6 +135,9 @@ subprojects {
       } else {
         compile externalDependency.hadoop
       }
+      compile(externalDependency.guava) {
+        force = true
+      }
     }
   }
 
diff --git a/conf/gobblin-env.sh b/conf/gobblin-env.sh
new file mode 100755
index 00000000000..384eafb935a
--- /dev/null
+++ b/conf/gobblin-env.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+# Set Gobblin specific environment variables here.
diff --git a/conf/gobblin-mapreduce.properties b/conf/gobblin-mapreduce.properties
index 9f5d09a637d..7636dfb2624 100644
--- a/conf/gobblin-mapreduce.properties
+++ b/conf/gobblin-mapreduce.properties
@@ -8,7 +8,7 @@ taskretry.threadpool.coresize=1
 taskretry.threadpool.maxsize=2
 
 # File system URIs
-fs.uri=file:///
+fs.uri=hdfs://localhost:8020
 writer.fs.uri=${fs.uri}
 state.store.fs.uri=${fs.uri}
 
diff --git a/gobblin-runtime/src/main/java/gobblin/runtime/mapreduce/CliMRJobLauncher.java b/gobblin-runtime/src/main/java/gobblin/runtime/mapreduce/CliMRJobLauncher.java
index 9af01788c61..52245e26894 100644
--- a/gobblin-runtime/src/main/java/gobblin/runtime/mapreduce/CliMRJobLauncher.java
+++ b/gobblin-runtime/src/main/java/gobblin/runtime/mapreduce/CliMRJobLauncher.java
@@ -23,6 +23,7 @@
 import org.apache.commons.configuration.PropertiesConfiguration;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.conf.Configured;
+import org.apache.hadoop.util.GenericOptionsParser;
 import org.apache.hadoop.util.Tool;
 import org.apache.hadoop.util.ToolRunner;
 
@@ -76,6 +77,11 @@ public static void printUsage(Options options) {
 
   public static void main(String[] args)
       throws Exception {
+    
+    Configuration conf = new Configuration();
+    // Parse generic options
+    String[] genericCmdLineOpts = new GenericOptionsParser(conf, args).getCommandLine().getArgs();
+    
     // Build command-line options
     Option sysConfigOption = OptionBuilder
         .withArgName("system configuration file")
@@ -100,7 +106,7 @@ public static void main(String[] args)
     options.addOption(helpOption);
 
     // Parse command-line options
-    CommandLine cmd = new BasicParser().parse(options, args);
+    CommandLine cmd = new BasicParser().parse(options, genericCmdLineOpts);
 
     if (cmd.hasOption('h')) {
       printUsage(options);
@@ -119,6 +125,6 @@ public static void main(String[] args)
         ConfigurationConverter.getProperties(new PropertiesConfiguration(cmd.getOptionValue("jobconfig")));
 
     // Launch and run the job
-    System.exit(ToolRunner.run(new Configuration(), new CliMRJobLauncher(sysConfig, jobConfig), args));
+    System.exit(ToolRunner.run(conf, new CliMRJobLauncher(sysConfig, jobConfig), args));
   }
 }