mkmf.rb: strip destdir from prefix

* lib/mkmf.rb (configuration): strip destdir part from prefix to get
  rid of duplication.  a patch by arton at [ruby-core:58859].
  [ruby-core:58856] [Bug #9213]

git-svn-id: svn+ssh://ci.ruby-lang.org/ruby/trunk@44019 b2dd03c8-39d4-4d8f-98ff-823fe69b080e