Pull up changes from Genome::Command::Base

In preparation for switching `Genome::Command::Base` to a `Command::V2`, this addresses some patches that were made to the former but not previously brought into UR.
I have a start to replacing STDERR in `_ask_user_question`, but `_get_user_verification_for_param_value_drilldown` uses `$self->status_message` currently, so that'll need to be reworked as well.  (In my quick test the question appeared but the choices went to `/dev/null`!)  If any commands out there also assume they can use `*_message` before asking a question they may be disappointed if we remove the `-t STDERR` test.