Add --engine to 'bundle launch' and 'bundle dry-run'
Update seqware script to pull non-snapshot JAR from the repo.  Allow overriding seqware version.
Make ini file optional in 'bundle launch'
Add specifying a destination directory to 'bundle package'
First pass updating command line examples to the new CLI. Surrounding text has NOT been updated.
Tpyo in doc.
Merge pull request #71 from SeqWare/feature/cli

Feature/cli