See GHC bug #1372
This is a consistency check, intended to prevent this class of build
failures:

   * Package P is updated, its version number is bumped, the
     new version is compiled and installed.

   * Package Q depends on P.  Q is modified to use the new P, and Q's
     .cabal file is updated with changes to the build-depends field to
     depend on the new version of P.

   * The user has an old build of Q.  They pull the changes to Q and
     'setup build' without cleaning or re-configuring.  Build errors
     ensue, because the code of Q depends on changes to P's API, and
     we're still building against the old P.

Note that you can't get segfaults this way, only build errors.

This also relies on some new consistency checking in GHC 6.8 to work
properly.  If the user re-configures their Q build and then issues
'setup build' without cleaning, GHC must now realise that the package
flags have changed, and re-compile all the affected Q modules.  GHC
6.6 would not do this, but 6.8 does.