CWL v1.0.1 spec support

Major release corresponding to v1.0.1 spec revision.

Behavior changes:

• default now applies when value is null to conform to v1.0.1
• "path" of files staged to InitialWorkDir is now in the working directory, not input staging directory.

1.0.20170525215327

• Fix --cache-dir
• Fix reading input object from stdin
• Support docker image repositories that include a port number
• Check for valid version of nodejs
• Fix bug workflow deadlock

1.0.20170510165748

Allow mutation manager to be optional. (#377)

1.0.20170510151339: Updatable inputs (#317)

* Implement mutation manager to validate that files can be safely modified in
place.

* Test workflows for mutable inputs.

* Add in-place update tests.

* Set up Docker binds to support writable items.

* Inplace update works with & without Docker.

* Add InplaceUpdateRequirement.

* Refactor job to split Docker and non-Docker execution into separate classes.

* Manage readers for inplace updates.

* Record readers, last update step.

* Downgrade validation warnings when checking input & output objects.

* Recursive copy (#356)

* Better handling for relocating directory outputs to final output.

1.0.20170413194156

Fix mergedirs() so it doesn't fail if a Directory object lacks a list…

1.0.20170413151007

Relax version dependency on python-six to 1.8.0 (#365)

1.0.20170329142446

Add ids to tools embedded in 'run' fields. (#354)

1.0.20170327143622: Rename loadListing enum (#349)

* Rename loadListing enum: no_listing, shallow_listing, deep_listing.

1.0.20170308174714: Mark LoadListing as not in vocab so it must be fully qualified (#324)

* Mark LoadListing as not in vocab so it must be fully qualified and not a
keyword.

1.0.20170224141733: Make "writable" flag apply recursively. (#301)

* Make "writable" flag apply recursively.