Change Mutant::Killer#run_with_benchmark to use Benchmark.measure

* Use the real time temporarily to be consistent with the other
  places in the code that measure time. When those other areas can
  be wrapped in a Benchmark.measure block all the benchmarks will be
  updated to use cpu time, not real (elapsed) time like now.

config/flay.yml

@@ -1,3 +1,3 @@
 ---
 threshold: 16
-total_score: 607
+total_score: 604

lib/mutant.rb

@@ -1,3 +1,4 @@
+require 'benchmark'
 require 'set'
 require 'adamantium'
 require 'ice_nine'

lib/mutant/killer.rb

@@ -89,10 +89,10 @@ module Mutant
     # @api private
     #
     def run_with_benchmark
-      start_time = Time.now
+      times = Benchmark.measure do
         @killed = run
-      end_time = Time.now
+      end
-      @runtime = end_time - start_time
+      @runtime = times.real
     end
 
     # Run killer