Read values for a handful of options in the new way.

Provides an example for mass migration.

Also fixes an issue where we weren't "descoping" old-style options
in all the places they could appear.

Reviewed in https://rbcommons.com/s/twitter/r/1114/
Sync of https://github.com/pantsbuild/pants/commit/e733dfaf8294cbdcf9946307385ba4a20531968d