Hello All. Some time ago I mentioned that I've got patches for full autotools support - here is the first patch in a patchset for your further consideration:
https://github.com/lemenkov/flashrom/commits/autotools
It was tested on RHEL 5, 6, Fedora 1x, i386, i586, i686, x86_64 and ppc (I'm using it for building Flashrom's RPM for a half of the year at least).
It's rebased on top of svn1412 and cleaned up to be a full drop-in replacement for handmade Makefile. Unfortunately I didn't test in on anything else than Linux, so I must admit that it's not in a very good shape for MinGW / BSD / DOS / Darwin users (ARM, MIPS users could be also hurt as well - that's why I didn't touch anything else in this commit except adding these two files).