Consistently use encode_with for YAML serialization

Puppet serializes objects to YAML using both to_yaml_properties:

lib/puppet/graph/simple_graph.rb

lib/puppet/parser/yaml_trimmer.rb

lib/puppet/resource/status.rb

lib/puppet/resource.rb

lib/puppet/transaction/event.rb

lib/puppet/transaction/report.rb

and encode_with (provided by PsychSupport):

lib/puppet/indirector/request.rb

lib/puppet/node/facts.rb

lib/puppet/node.rb

lib/puppet/resource/status.rb

lib/puppet/util/log.rb

This is bad for a few reasons:

1. Relying on YAML#to_yaml_properties has been deprecated since ruby 1.9.3
2. Note that Puppet::Resource::Status defines both to_yaml_properties and uses encode_with. As a result the serialization behavior depends on the ruby version and YAML engines (Syck vs Psych) and the 2 serialization methods could serialize different instance variables.
3. Ruby 2.1 changed how Array subclasses are serialized, and Ruby 2.3 does the same for
Hash subclasses. Note the ivars and the hash-with-ivars tag:

--- !ruby/array:MyArrayObject

internal:

- 1

ivars:

  :@foo: 2

--- !ruby/hash-with-ivars:MyHashObject

elements:

  1: 2

ivars:

  :@bar: 3

This means YAML data written by an agent running ruby 2.3 may not be readable by puppetserver using JRuby 1.7 (which is compatible with MRI ruby 1.9.3).

Puppet should consistently use PsychSupport and its encode_with methods. Similarly, we should be using init_with and leveraging the from_data_hash methods to deserialize instances. This ensures that objects explicitly state which data to serialize, and ensures that object initializers and setters are called during deserialization, instead of using bypassing that with instance_variable_set.

See discussion in https://github.com/puppetlabs/puppet/pull/4214#issuecomment-138691121

/cc Henrik Lindberg, Geoff Nichols, Ethan Brown