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.
I think the problem with just moving this file is that the `.jenv` file will be left lying around. We need to remove that local file if it was created and we cannot bootstrap.