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:

* [x] Moar specs.
* [ ] End to End bootstrap testing
* [ ] CHANGELOG and RELEASE_NOTES updates.
@sersut `Chef::Config[:knife]` gets merged into the mixlib-cli `config` object here: https://github.com/opscode/chef/blob/master/lib/chef/knife.rb#L314-L323