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Just looking at the manual/.symlinks file, it looks like it might be
missing several needed links? I tried to update what I could, and a
patch with my changes is attached.
As for Automake and Autoconf specifically, symlinks look like they're
being made, but the links are using a capital A for the first letter
(Automake.html and Autoconf.html, instead of automake.html and
autoconf.html). I wasn't sure how to change those properly in the CVS
source code, so the patch does not include changes for these links.