blackbox: fix recording exit codes (issue3938)
Previously the blackbox wrapped runcommand, but this failed to see the error
codes that were created if an exception occurred. I moved that logging to now
wrap _runcatch, so it can observe and log the actual error code (such as when
a user ctrl+c's during a command).
Updated the tests as well. Tested the change by running all the tests with the
blackbox extension enabled and verifying nothing broke (aside from things that
printed what extensions were enabeld).
The progress tests are affected by calls to time.time() so they needed to be
updated to pass.