Remove Genome::Command::Base

It's features were incorporated into `Command::V2`, so use that everywhere instead.

* The module `Genome::Env::GENOME_NO_REQUIRE_USER_VERIFY` is still here at the moment, but the variable now has no effect.
* There's a new `Genome::Command::Base` that's the parent of `Genome::Command` and `Genome::Model::Tools`.  It probably shouldn't be the parent of a new tool added to the tree--`Command::V2` should be!