Feature/seqware 1400 continued oozie improvements

I pulled this into the AMI and did the following to test it:

# just build like normal, I did not run all the regression tests
mvn clean install -DskipTests

# create a HelloWorld
mvn archetype:generate

# Pegasus HelloWorld
mvn install -DskipITs=false
 
# Oozie Engine, this works! Input/output to normal filesystem
java -jar /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT/Workflow_Bundle_HelloWorld/1.0/lib/seqware-distribution-1.0.0-SNAPSHOT-full.jar --plugin net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher -- --no-metadata --provisioned-bundle-dir /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT --workflow HelloWorld --version 1.0 --ini-files /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT/Workflow_Bundle_HelloWorld/1.0/config/workflow.ini --workflow-engine oozie --wait

# Oozie but reading/writing to HDFS
hadoop fs -put /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT/Workflow_Bundle_HelloWorld/1.0/data/input.txt /tmp/

# the config changes
input_file=hdfs://localhost/tmp/input.txt
output_prefix=hdfs://localhost/tmp/

# run it
java -jar /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT/Workflow_Bundle_HelloWorld/1.0/lib/seqware-distribution-1.0.0-SNAPSHOT-full.jar --plugin net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher -- --no-metadata --provisioned-bundle-dir /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT --workflow HelloWorld --version 1.0 --ini-files /mnt/databases/workflow-dev/HelloWorld/target/Workflow_Bundle_HelloWorld_1.0_SeqWare_1.0.0-SNAPSHOT/Workflow_Bundle_HelloWorld/1.0/config/workflow.hdfs.ini --workflow-engine oozie --wait

# it works!
hadoop fs -cat /tmp/seqware-results/output
Hello World!