(PUP-3593) Address SSL cleanup and puppetserver restart timing issues in acceptance tests.

@hlindberg Here's the commit with a refernce to the JIRA ticket.
What case is this handling?  Is it not possible to to issue a `puppet cert clean some.cert` command on a puppetserver master?  That seems like it breaks our general instructions for resetting an agent's certs (rm the agent ssldir and issue the puppet cert clean for the old cert on the master).