Set ALTERNATE_FROM_CLASS in command-line entry points.
Stop using Genome::Command::Base.

Its features are now in UR's Command::V2.
Remove Genome::Command::Base.
Formatting changes to help docs so can be parsed as verbatim POD.
Pull up setting alternate classes to a new Base.
Warn if using old GENOME_NO_REQUIRE_USER_VERIFY variable.
Merge pull request #228 from tmooney/deduplicate_gcbase

Switch over remaining uses of Genome::Command::Base to Command::V2.

CHANGELOG:  The GENOME_NO_REQUIRE_USER_VERIFY environment variable no longer has any effect and will be removed in a future snapshot.  Control of prompting is consolidated into the existing UR_NO_REQUIRE_USER_VERIFY variable. The UR version of the variable should be used in all cases where the GENOME version was previously.