Yes, cert-store has to do with storing the certificates pan receives for
a secure connection, so indeed, it's ssl-related.
My guess is that it's still finding the old include files since you
didn't mention moving them or editing the *.pc file. The *.pc file
should give the correct paths, but in the actual compilation, it's likely
the system paths are coming first, in ordered to be able to find other
libs, so the build is using the headers in those system paths, which are
still the old headers since that version wasn't removed.
Meanwhile, in the other subthread you mentioned possibly building the new
version, pointed at the system location, thereby replacing the old one
already there. That should work for pan since you're rebuilding it now,
but do be aware that it may well break other apps/libs depending on
gnutls. They'd likewise be fixed with a rebuild (possibly with a patch
or of a newer version), but I'd at least check to see what packages you
actually have linked against gnutls, so you have some idea of how big the
hole you're digging might get.
That's one good thing about gentoo and similar managed-build-from-source
distros. Since everything's built from source, and at least gentoo has a
tool called revdep-rebuild that can automatically scan for such broken
dependencies and tell you what to rebuild, breaking such dependencies due
to update is no big deal, you simply run the tool and let it rebuild what
it needs to, afterward, and since everything's built from source already,
there's no worry about having to manually bring in whole lists of missing
build dependencies and resolve everything one manual build and test at a
time. I remember running mandrake and having to do that manually, and
how nice it was when I first started on gentoo, having it all "just
work", because the whole set of assumptions were different when you were
building /everything/ from sources.