The python-augeas errors are a known issue with an upstream release of python-augeas that has problems. People who had their certbot-auto auto-update may have encountered this bug, through no fault of their own. Some of the developers told me earlier today that if they let certbot-auto auto-update once again, the problem should now be fixed.
If not, please let me know and I’ll pass the error report along.
You are likely using an old version of letsencrypt-auto from before we pinned versions of python-augeas. Replacing that script with https://dl.eff.org/certbot-auto (or downloading from any other certbot source) and running as before should fix this issue.