Write fab test job stdout and stderr to a file.
Consolidate test data dir location in tests.
Add chunked mode to running integration tests via fabric.
Re-enable --distributed and --chunked in commandline options. Better argparse usage statement and display of outputs.
Very Minor fix to docs to remove sphinx warning.
Added DevTest Pmodule for testing new ReferenceEntry SMRTFile.
Attempt to tighten up the WorkflowSetting initialization. The job_output_dir is requied positional arg now. Updated all unittests. This introduces a bit of oddness in the IO layers when parsing the input.xml and workflow.xml files. However, the WorkflowSettings are always initialized correctly now.