I haven't ever used autogen.sh in my previous installs. I use:
[...]
If you compile from the ckolivas' source tarball, the configure script is (probably) included and you don't need to run autogen.sh. If you use kano's link, which seems to be simply his git repo packaged, you need to run "./autogen.sh" right before the configure step, as the configure script isn't included in the git repository.
Simply run:
cd ~/cgminer-2.XX/
./autogen.sh
CFLAGS="-O2 -Wall -march=native" ./configure