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Anyway, since this bundled libtool looks like it's very recent it doesn't make sense to try to forcibly autoreconf it to something older, as cygautoreconf seems to want to run autoreconf --force. Normally autoreconf would only run libtoolize if it looks like something needs updating. So I guess what I'm saying is just remove cygautoreconf from your cygport, or if it's needed for some reason, don't run --force.
I didn't try without cygautoreconf, cygport insists (hardcoded) on using --force in the autoreconf command. Using the following patch
--- /usr/bin/cygport.org 2008-03-17 17:30:33.745423700 -0400 +++ /usr/bin/cygport 2008-03-17 17:17:50.856572500 -0400 @@ -976,7 +976,7 @@
for d in . ${ac_subdirs} do
Brian
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