The libchipcard ebuild creates the (empty) directories /usr/lib/chipcard2-server/lowlevel /var/lib/chipcard2/newcerts /var/log/chipcard2 which are needed by the server. That's fine, but when you upgraded libchipcard, the unmerging of the old version will delete them again because they are empty. I guess there's some kind of .keep file needed; for the newcerts directory a 'chipcardd2 init' might provide reasonable defaults, too.
keepdir added, certs aren't strictly required, so I think it's up to the user if he needs them.
