Fix some restart script issues found with certificate renewal.
The restart_dirsrv script wasn't initializing the api so the
startup_timeout wasn't available.
The subsystemCert cert-pki-ca definition was missing so we didn't
know which certificate to update in CS.cfg.
Add some documentation and a pause between restarts for the
renew_ca_cert script so that when the CA subsystem certs are renewed
they don't all try to restart the CA at the same time.
https://fedorahosted.org/freeipa/ticket/3006