remaining issues for the CWL Expression extractor/transformer

[Michael R. Crusoe]

from #5

• add tests
• support saving new copies of external tools adjacent to the original one, or into a target directory
• Teach schema-salad's codegen tool to serialize in a better order (separate issue?)
• run all CWL v1.0 conformance tests to check for corner cases ; moved to #45
  • the above, but cwltool --pack first
• expose the option to only replace CWL expressions and leave ExpressionTools as is via a command line flag
• consolidate so there is only one ExpressionTool/CommandLineTool generated by this script per Workflow and per WorkflowStep. The later will combine any step level and Process level additions needed ; moved to #49
• make a CWL v1.1 version of the script

[Michael R. Crusoe]

The remaining open issues have been transferred to stand-alone issues