I am very sorry, but I cannot provide you with any specific reason, I sadly mostly script and am rather insightless into programming and related file management, so I cannot really be partisan on this issue. What they said is simply that different kinds of files belong in different places, and that putting everything in one place is bad practice, but that they are used to seeing this on scientific software packages. They also suggested I re-write the makefiles, but I currently lack both the knowledge needed to do so and the time needed to acquire that knowledge.

In a related matter, this tutorial [lcni.uoregon.edu] seems to suggest that I only have to keep the linux_glibc32/ (or is it in my case the linux_fedora_19_64/ ? ) directory. Is that so? (doesn't look like it)

1) is there any way to pull directly from your CVS repository?

3) Yes, I was asking because I need to know whether I have to add a PATH entry for afni under root etc/env.d - as I understand, if I do not, binaries will not be callable by name alone, but only as /opt/afni/.../binary - which, as the Gentoo maintainers told me, will break if afni binaries call each other.

4) Until you are able to do it - the suite will work anyway, right?

Many Thanks for Your Help,
Christian