Allow deployment of setup/

Useful for initial installs, where deployment of the `setup/` folder is
required for the initial install. Thereafter, deployment can be run without
the setup option so that the rest of the codebase can be maintained (already
supported)
Merge pull request #750 from greezybacon/feature/deploy-setup

Allow deployment of setup/

Reviewed-By: Peter Rotich <peter@osticket.com>