Secondary index collections test, and changes to handle unready connections without needing pauses

I was hoping to make the 'patient_cql_connection' part of tools.py but that would require the tools functions to know about the internals of the Tester class which I didn't like.

The patient_cql_connection method is just a wrapper that calls the original cql_connection method, so the change won't impact any tests using cql_connection, but now we can move flaky tests over to the 'patient' version and hopefully get better feedback from test runs.

The test for secondary indexes on collections is pretty basic, but due to one bug reported on CASSANDRA-4511 it will currently fail.