mkmf.rb: remove extra topdir in VPATH

* lib/mkmf.rb: remove extra topdir in VPATH, which was in
  win32/Makefile.sub for some reason and moved from there.
  [ruby-dev:46998] [Bug #7864]

git-svn-id: svn+ssh://ci.ruby-lang.org/ruby/trunk@39290 b2dd03c8-39d4-4d8f-98ff-823fe69b080e