The cygbuild script still has JOEVERSION=3.5 and CYGVERSION=3.5-1 (and the comments still have 3.3 in the tarball names).
I've modified the autoconf and automake stuff so that you have more control over where the files go during the installation.. this was triggered because I saw recent version of joe in cygwin have the joerc files in /etc/joe, but the syntax files in /usr/share/joe and extra documantation in /usr/share/doc/joe.
Anyway, you need to update autoconf, automake and m4 if your autobuild tools are two years old like mine. Otherwise it tries to install the extra documentation in /. (this is only an issue if you are building from cvs).
Also, I've bumped up the rev in cygbuild 3.6, but I think it's going to be 3.7 before I actually give it to cygwin.
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