Changed cert_db to use Certificates and log_ids.

I think it's nicer if cert_db itself pulls subject names etc. from the certificate, so I changed it to use cert.Certificate. Also it should be more convenient if id in database were the same as certificate index in log.
Can't it be done in the __init__ / setUp methods?
Seems like most methods in this class would require the default init.
Do this as a default in the test setup, and in the few test cases where you don't need this, just create a new db.