Support for running a workflow test without an ini file
- For example, if an ini file and parameters are not specified in the test json, the workflow test will be run with the workflow's default parameters
- In the case where the ini file is not specified, an "id" should be set, and the metrics file should be name <id>.metrics.  Override this be specifying "metrics_file" (either full path, or the file name in "output_metrics_dir").
Merge pull request #7 from pipedev/PDE-502

Support for running a workflow test without an ini file
Support for multiple ini files; Parameters temporary workaround
- "parameters" specified via the json workflow test definition may not be interpreted correctly from the seqware command line
- as a workaround, parameters are saved to an ini file which is passed to the seqware command line
- this also required that multiple ini files be supported by the testing framework
- improved logging in Helpers isFileAccessible
Merge pull request #8 from pipedev/PDE-502

Support for multiple ini files; Parameters temporary workaround
Merge branch 'develop' into PDE-743

Conflicts:
	common-utilities/pom.xml
Merge branch 'PDE-743' into develop
Reorganization of JSON validation code and tests
Merge pull request #10 from pipedev/PDE-502

Reorganization of JSON validation code and tests
Improved performance and logging of FileProvenanceReport parsing
- Two validation modes are supported during parsing: string or skip.  Strict mode will throw an exception and exit if there is an error, skip will log an error and continue.
- For every 10000 records, a message will be printed to give the user an update of the process.
- Moved to log4j2 logging framework.
- Parent samples are now transformed to an object (rather than storing its seqware string representation).