Apply isort.
Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
This has been rebased several times and includes a variety of fixes (some thanks to martenson).