menuselect: Fix check for running configure.

menuselect/Makefile checks that autoconfig.h and makeopts were newer
than the '.in' files.  Unfortunately running ./configure does not touch
autoconfig.h unless the contents will change.

Instead of looking at autoconfig.h we just need to ensure that makeopts
is newer than configure.

Also make change to configure.ac so bootstrap.sh doesn't re-add the
extra trailing line-feed.

Change-Id: Ief1f831d6717007f9cebb668c14e92782cd2b794