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
period to end the sentence, please.

Also, while you're here, can you please move this defer above the `if c.MetadataSource == "" {` block above. That case would have left the .jenv file lying around.