I'm glad it is all compiling now.
Did the Gentoo people actually tell you why they mind
keeping the entire compile directory? That is what we
generally suggest, since it makes our lives easier,
though I can certainly imagine it is not preferable for
distribution maintainers. But still, a reason would be
nice to hear.
There are over 500 programs, models and plugins in the
output build directory. It does not seem like a good
idea to put that in a directory with anything else.
1) We actually use the build date as a version, since
CVS did not do the versioning the way we hoped. We
usually ask for the 2 lines from "afni -ver" for it.
Alternatively, "afni_history 1", shows the last change.
2) No, write permissions are not needed. AFNI is very
often installed as root.
3) I do not understand your initial question. Yes,
many AFNI programs call others, though it is generally
sufficient that they are in the path. One ugly thing
we do is put template datasets there, though there is
a good mechanism to do otherwise.
4) Those functions do not seem to have prototypes from
any #include statements. I will add an include.
- rick