Refactor directory hierarchy

Refactored the Puppet code so that it is all self-contained inside the `puppet/` folder in order to avoid potential conflicts with any other projects that are based off this automation.

This includes relocating:
* `Rakefile`
* `Gemfile` & `Gemfile.lock`
* `Puppetfile` & `Puppetfile.lock`

since these file should remain Puppet-specific and independent of any other `*file`s that may be required later that have nothing to do with the environment automation.