cygport autoreconf --force step stomping on perfectly good config.guess file

[Warren Young]

In trying to get sqlite3 built for 64-bit Cygwin, I've run into a wall: 
during the cygport compile step, it runs

     autoreconf --force -i --verbose

This overwrites the config.guess shipped with SQLite with the one from 
automake 1.9.  (I know this for a fact based on file sizes.)  That old 
version doesn't understand Cygwin 64, so it gives a verbose error that 
amounts to "upgrade, dude."  If autoreconf were to grab the config.guess 
from automake 1.13 or the one shipped with Cygport itself, all would be 
well.

I'm guessing this happens due to this line in SQLite's configure script:

     am__api_version="1.9"

I can't run autoconf to re-generate this, since the configure.ac file 
has a bunch of old constructs that autoconf 2.69 barfs on.

I don't want to suppress the autoreconf step, since the SQLite tarball 
*also* includes an outdated config.guess script.  So, autoreconf *does* 
need to be run.  It just needs to be made to DTRT.

My subject line refers to the fact that even if I copy a good 
config.guess file in by hand between the prep and compile steps, 
autoreconf overwrites it anyway, probably because of the --force flag.

Ultimately, upstream should upgrade their autotools and fix their .in 
and .ac files, but seeing as how they just applied a trivial patch I 
provided 3 years ago, I'm not going to hold my breath waiting.

Any suggestions on how to fix this without involving upstream, and 
without wholesale replacement of the autotools input files shipped with 
the SQLite tarball?

My guess is that it would be best if I could slip a custom step in 
between the 'autoreconf' step and the 'make' step, hand-copying in an 
up-to-date version of config.guess from somewhere.  Does cygport have 
such a hook?

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