This commit sets the structured_facts option to nil if its still
UNSET_VALUE at the finalize step. This was causing a bug when the facter
config was set but was not using structured facts.
Prior to this commit, the puppet provisioner would use the manifest dir
flag when running `puppet apply`. Not only is this flag redundant due to
how puppet apply works, but it is also deprecated in Puppet 4 and
removed in Puppet 5. This commit simply removes the flag when invoking
`puppet apply`.