layout as we always had in trees containing only the builtin
2) win\configure.js WITH_INNOBASE_STORAGE_ENGINE still works.

storage/innobase/CMakeLists.txt:
  fix to new directory name (and like 5.1)
storage/innobase/Makefile.am:
  fix to new directory name (and like 5.1)
storage/innobase/handler/ha_innodb.cc:
  fix to new directory name (and like 5.1)
storage/innobase/plug.in:
  fix to new directory name (and like 5.1)