Chef 12 bootstrap cleanup

* Cleans up deprecations for Chef 12
* Implements the encryted data bag secret distribution based on [this](https://gist.github.com/sersut/94c8daad5c11369bd2e8) 
* Simplifies the bootstrap CLI options slightly.

@opscode/client-engineers wanted to share this before increasing the spec coverage around these options. 

Remaining work:

* [ ] Moar specs.
* [ ] End to End bootstrap testing
* [ ] CHANGELOG and RELEASE_NOTES updates.
I think the check is OK, unless someone can give a good reason as to why we shouldn't automatically set `:encrypted_data_bag_secret` based on its presence...

If we set a non-nil default value here, we'll have to modify the logic in [Chef::EncryptedDataBagItem::load_secret](https://github.com/opscode/chef/blob/master/lib/chef/encrypted_data_bag_item.rb#L128-L153). I'm in favor of having some kind of default global variable that stores `"/etc/chef/encrypted_data_bag_item"` for use in cases where `Chef::Config[:encrypted_data_bag_secret] == nil`.