net/freeipa-server: Fix hardcoded paths

ipa-cacert-manage, ipa-getcert and the chrony tools were taken from the
Linux defaults, so they pointed at /usr/sbin, /usr/bin and /etc, where
FreeBSD has nothing. ipa-client-install aborted at the time
synchronisation step for that reason. net/chrony was missing from
RUN_DEPENDS as well.

Reported by: m87carlson (via my private GitHub FreeIPA repository)
Sponsored by: Netzkommune GmbH