Update and run isort (#9573)

I want to use isort as part of https://github.com/certbot/certbot/issues/9572 because I want to do it programmatically, however, I felt like the config needed to be tweaked a bit due to it not understanding what is and is not our own code.

This PR updates the isort config so it recognizes our own modules and runs `isort .` from the root of the repo to update everything.

* update isort config

* run "isort ."

certbot-apache/tests/util.py

@@ -1,10 +1,10 @@
 """Common utilities for certbot_apache."""
 import shutil
 import unittest
+from unittest import mock
 
 import augeas
 import josepy as jose
-from unittest import mock
 
 from certbot.compat import os
 from certbot.plugins import common