Fix errors made when merging the new Boehm GC.

boehm_gc/misc.c:
    As above.
Make it possible to build boehm_gc and libatomic_ops as part of Mercury.

Now that we're using the git source for boehm_gc and libatomic_ops rather
than source tarballs we need to ensure that certain extra files are
generated before building, specifically ltmain.sh.

boehm_gc/autogen.sh:
boehm_gc/libatomic_ops/autogen.sh:
    Call libtoolize prior to setting up autotools.

boehm_gc/build_atomic_ops.sh:
boehm_gc/build_atomic_ops.sh.cygwin:
    Call libatomic_ops's autogen.sh script.

boehm_gc/configure.ac:
boehm_gc/libatomic_ops/configure.ac:
    Configure libtool (and other things) to use the current directory as
    their auxiliary directory (where ltmain.sh should be put), rather than
    the Mercury directory.
Make changes required to upgrade to Boehm GC 7.4.2

GC_stackbottom, GC_gc_no and GC_dont_gc are now deprecated.  These changes
use new options in the API where possible.

Update scripts to copy the boehm_gc directory correctly.

Pase Boehm GC the correct flags for thread support

Update documentation regarding the version of Boehm GC.

runtime/mercury_wrapper.c:
    Don't use the deprecated GC_dont_gc variable.

library/benchmarking.m:
    Use GC_get_stackbottom() to get the bottom of stack and GC_get_gc_no()
    to get the number of collections so far.

util/mkinit.c:
    Do not explicitly set GC_stackbottom anymore, except on AIX where it
    cannot be found automatically.

scripts/prepare_install_dir.in:
stools/bootcheck:
    Add some missing files present in Boehm GC 7.4.2 that wern't present
    earlier and remove some old ones.

.README.in:
bindist/bindist.README:
    Update documentation regarding the version of Boehm GC.

compiler/notes/upgrade_boehm_gc.html:
    Documentation fix

configure.ac:
    Something in Boehm GC's build system has changed and we must now pass
    -DGC_THREADS whenever building threadsafe versions of BOehm GC.  This is now
    done using the BOEHM_MISC_CFLAGS_FOR_THREADS autoconf variable, which has
    been renamed to BOEHM_CFLAGS_FOR_THREADS now that it is more generally used.

    Boehm GC no longer (or perhaps never did) require developers to specify the
    type of threading to use, eg -DGC_LINUX_THREADS rather than -DGC_THREADS.
    With the exception of win32-pthreads.  We now pass -DGC_THREADS whereever
    possible.

Mmake.common.in:
    Rename BOEHM_MISC_CFLAGS_FOR_THREADS.