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 see; yes this is exactly why the second clause of that warning above was there. Without a semaphore (I agree with a file-lock; it would be cross-platform as well), I didn't see how we could reliably clean up data without knowing if it was our data to clean up. If I can introduce a semaphore, I can effectively separate these two cases and handle them correctly.

FYI, I am looking at another bug (https://bugs.launchpad.net/juju-core/+bug/1336843), and I may want to handle the second case there.