Version 0.4.0 release candidate 1

This is the second release candidate for neurodocker version 0.4.0.

Fixes

• pip installation (previously, the required yaml files were not being installed).
• matlab compiler runtime uses https urls
• documentation is fixed and all examples are functional
• examples are updated to new command line interface

Adds

• --run-bash command line option

Users of this release may notice that features may be have dropped while converting from the old class-based to the new template-based framework. This is not intentional in most cases, so please submit an issue if a feature that you use has been lost.