Rebuild puppet manifests properly with modules and use bin/update

Summary:
- Rebuild puppet manifests properly with modules
- Add --no-dev and --no-git args to bin/update

Refs T296

Test Plan:
Run `bundle install` (to get librarian-puppet installed)
Run `librarian-puppet install`
Run `vagrant destroy` then `vagrant up && vagrant provision`

Reviewers: bodacea, rjmackay

Reviewed By: rjmackay

Subscribers: shadowhand

Maniphest Tasks: T467, T296

Differential Revision: https://phabricator.ushahidi.com/D253