Bootstrap no longer cleans up if it can't tell whether an environment is bootstrapped or not.

Added a test to simulate an instance in which this might occur. Tested locally; some tests were failing, but they looked innocuous and related to connecting to mongo, not these changes.
Related to https://bugs.launchpad.net/juju-core/+bug/1340893
I'd skip the note about cleanup on the end here, this isn't a message we expect users to hit in normal operation (unlike just running bootstrap twice or similar).