[CHEF-4509] read `secret` `secret_file` from knife hash

The new config values for specifying a raw secret or path to a secret
file were being incorrectly read from the top-level of the `knife.rb`
config keys. This commit fixes things to correctly read from the knife
hash as documented here:

http://docs.opscode.com/config_rb_knife.html
https://github.com/opscode/chef/blob/11.6.0/lib/chef/knife/bootstrap.rb#L262
/me a pedant, fix indention level in options
Merge pull request #1060 from opscode/CHEF-4509

[CHEF-4509] read `secret` `secret_file` from knife hash