I don't know much about autogen, but here are my observations:
Using the wiki as a guide, I checked out https://kibadock.svn.sourceforge.net/svnroot/kibadock/trunk/akamaru. First thing I did was run:
joe@vostro $ ./autogen.sh
After running aclocal, the following error message appears:
configure.in:51: error: AC_SUBST: `"$AKAMARU_REQUIRES"' is not a valid shell variable name
After some research, it looks like I was able to fix the problem. I replaced "$AKAMARU_REQUIRES" with AKAMARU_REQUIRES. Now it works. Attached is a patch I made for configure.in.
I am running the following version of aclocal:
aclocal (GNU automake) 1.10.1
patch for configure.in that fixes the AC_SUBST problem