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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