Merge pull request #1 from curoverse/master

Reference implementation
Cwltool outputs json object with stdin and stdout.  Test includes stdout.
Better logging by test running.
Add test runner.  Improve documentation.  Add return codes.
Improve reporting in run_test.sh a little bit more.
Setup.py works.  Improve documentation.
Update documentation to provide a brief guide to the various subdirectories of
CWL repository.
Add links to CWL implementations.
Cwltool supports nested adapters.  Added $job (sort of like $ref but references
the job document.)  Added tmap to conformance test.
Added wfdesc example of Nebojsa's Rabix workflow

<examples/bwa-and-freebayes-workflow-wfdesc.json>
pav:derivedFrom <https://groups.google.com/d/msg/common-workflow-language/oIWTGq3rHcw/9d0q0FjJqMQJ> .
Merge pull request #2 from stain/wfdesc

Added wfdesc example of Nebojsa's Rabix workflow
Adding more examples.  Started work on running jobs in Docker.  Working on
capturing and remapping file paths.  Fiddling with ref resolving of cross
references in schema files.
Merge branch 'master' of https://github.com/rabix/common-workflow-language
Remap file paths to absolute paths by default.  Accomodate this in conformance test.
Added filename mapping for running inside docker.
* Docker running works!  Supports bind mounting input and output directories and
stdin and stdout redirection.
* Conformance testing now requires --basedir (to standardize the absolute
directory path that is generated) and --no-container to suppress container bind
mount name remapping.
Not used.