I see you applied to scons changes. Should I do something similar for autoconf?
The changes are all about 'scons install'. It installs to /usr/share/doc/lyx and /usr/share/Cygwin/lyx-1.4.3-1 some doc and readme files. It would be nice if autotools can also install in this way, although to use autotools, some tricks in the wiki (primarily about the link script) should be used. Cheers, Bo