@avalos My note-taking setup, while not checking all those boxes, comes close: I use Emacs with Deft to write my notes (Markdown or Org Mode with optional LaTeX support), and they're saved to a Keybase git repository, which encrypts and decrypts transparently on the fly, and syncs it to the Keybase git remote. I have a little Ruby Guard script that automatically does a git commit and push anytime I hit save in Emacs. It's worked really well for me for around 4–5 years now.
@avalos It's not very hard to set up, but if you're looking for something out-of-the-box, you might like “Standard Notes”, which lets you write notes, with end-to-end encryption, and syncs them to the cloud automatically. It's available on all platforms, and on phone as well. https://standardnotes.org/
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