For PR614:

Move the implementation of the fix from Makefile.rules to Makefile. This
ensures that it is only checked on a top-level rebuild, and not in every
single subdirectory. This removes some annoying messages from the build and
numerous executions of config.status if the .in file changes but not
substantively enough to cause the .h file to be modified by config.status.

llvm-svn: 23039