(PUP-3312) Remove deprecated methods from the Puppet module

This commit removes the `parse_config` and
`initialize_settings_for_run_mode` class methods from the Puppet
module. This commit is part of the code removal effort for Puppet 4.
Merge pull request #3284 from whopper/pup-3312/removal/puppet-module

(PUP-3312) Remove deprecated methods from the Puppet module