>> 4. In an empty build directory (~/emacs/build), run
>> "CPPFLAGS='-DGLYPH_DEBUG=1' CFLAGS='-O0 -g3' ../repo/configure
>> --enable-checking".
>
> Please also test with caching (-C) enabled, since AFAICS the only
> difference to the current situation is that the relevant settings are
> now applied after any cache is read.

It works also with -C (I've just tried it).

>> +test "$MSYSTEM" = "MINGW32" && source $srcdir/nt/mingw-cfg.site
>
> This should be "." rather than "source", since that is what configure
> uses to read CONFIG_SITE (IIRC it's more portable).

Ok.

> Can you also supply the necessary doc patches (mainly nt/INSTALL)?

See the attached patch.  (the change to 'nt/mingw-cfg.site' needs
refilling; I've not done it to make my change more clear)

The changelog entries could be something like this (feel free to make
your own adjustments):

For the root ChangeLog:

2013-11-08  Dani Moncayo  <dmoncayo@gmail.com>

	* configure.ac [MINGW32]: Add call to 'nt/mingw-cfg.site'.
	* make-dist: Don't make link to 'nt/msysconfig.sh'

For 'nt/ChangeLog':

2013-11-08  Dani Moncayo <dmoncayo@gmail.com>
	
	* msysconfig.sh: remove.
	* INSTALL:
	* mingw-cfg.site: The MSYS-specific configure script no longer exists.
	Instead, use the standard (POSIX) configure script.


-- 
Dani Moncayo