Bring up to date with current shell-command API (closes #61)

The current shell command service requires workingDirectory, which breaks most tests.

This is addressed using templates the test request bodies to provide `workingDirectory` based on a testing environment variable.

I also needed to pin the `flask-restful` dependency to pass tests.  I will leave pinning all remaining deps and integrating with [requires.io](httsp://requires.io) for another PR.

This closes #61 and may rely on genome/ptero-shell-command#22 to pass tests.