Hello, I have been working on packaging AFNI for Gentoo Linux for a while now, and, while the current ebuild (Gentoo package atom) works, it does so by cutting a lot of corners.

Among many other things, to make AFNI kind-of compile right, I have to hack one of the Makefiles with sed, and delete some of the stuff bundled in AFNI after it has been already compiled. I was thinking of fixing this by writing a Makefile that does not compile many of the bundled things in the first place. A recent comment over on github, however, made me doubt whether or not that is a worthwhile endeavor - since it is not only a lot of work upfront, but also quite a bit of work to maintain.

Is there maybe any interest with the AFNI developers to switch to CMake or Autotols? This would help not only me, but lots of other package maintainers better deliver AFNI to users. Also, I believe it would be easier for you to maintain in the long run, as well.