>When I want to reply to someone, do I email the list or the person? How do I make sure the emails are threaded properly?
Most people will (and you should, too) use reply-all when participating on a mailing list, which should land the replies straight into your inbox. Just reply-all to these normally, making sure not to top post. If someone makes a mistake, and you weren't subscribed to the list, the web archives usually have a mailto: link somewhere that you can click to reply to the thread.
>The git email client seems to have support for message IDs.
You should never have to directly work with message IDs if you're using git-send-email and letting your mail client handle replies.
>Also, gmail has moved on to newer authentication mechanisms.
They should still have support for SMTP PLAIN authentication unless you use gsuite and your admin has turned it off, if I understand correctly. I have written a mail client which has support for OAUTH, however, which you might find useful:
https://aerc-mail.org
I don't use gmail so if you run into problems, please reach out to the appropriate mailing list - I won't know how to help.
I would also, of course, strongly recommend that you ditch gmail ASAP.