remove puppet run stages

the puppetlabs apt module will already do an apt update for you so there is no need for run stages etc any more.

https://github.com/puppetlabs/puppetlabs-apt/blob/master/manifests/source.pp#L41

    Apt::Source <| |> -> Package <| |>

This sets a default ordering for all of the Apt::Source resources to be done before any Packages are managed.