def run(command, options = {})
      %x{ #{command_options_to_string(command, options)} }
    end
run a shell command and pipe stderr to stdout
@param [String] command
@option options [String] :out the IO redirect of the command
@option options [Hash] :env explicit environment to run command in
@option options [Boolean] :user_env whether or not a user's environment variables will be loaded