Init cli.
Implement more features.
First pass at create commands.
Fix logic bug in Module regarding argument quoting whereby a fully quoted argument and every subsequent argument would be lost.
Add bundle commands; remove inappropriate quoting of args to PluginRunner; expose --debug; temporarily removed visibility controls.
Update seqware script to use current snapshot seqware version, and pull from local maven repo.
Trigger interactive creation of seqware settings file.
Doc change
Better handling of password entry.
Actually pass arguments to main.
Handle propagating args with spaces
move debug flag handling
Note which fields have dynamic values
Add command to generate workflow ini.
First pass of updating tutorial with new CLI.
Rename how reporting works in CLI.
Enable console printing of workflow run report.
Handle relative dirs during packaging, since BundleManager doesn't.
Expose engine flag on workflow schedule.
Use "accession".