I love how convenient PuPHPet makes creating and maintaining your website's VMs but I hate how it adds two additional folders and three additional files to the root of our project.

It turns out there is a quick solution to this problem.

Create a new folder named Vagrantfiles and copy every file except the Vagrantfile into this folder. Then find this section of your Vagrantfile:

config.vm.provision :puppet do |puppet|
  puppet.manifests_path = "manifests"
  puppet.module_path = "modules"
  puppet.options = ['--verbose']
end

and change it to:

config.vm.provision :puppet do |puppet|
  puppet.manifests_path = "Vagrantfiles/manifests"
  puppet.module_path = "Vagrantfiles/modules"
  puppet.options = ['--verbose']
end

Now it's much cleaner so I can dump all the files I need for my project there. :-)