The best way to update an in-place install is to dump the actions, classes, lib, and plugins folders (backing up plugins you use first), and then reuploaded them, along with any additional plugins you used. This will ensure you don't have any duplicated files from the reorganization. You'll also want to run upgrade.php to verify database integrity as well.
If you're already on Nightly, then you've got all these changes to begin with of course, but there's a bunch of new stuff for those on Master.
As always, if anything explodes, ping me on the Fediverse and I'll try to help :)