I know it's fast becoming a trope or cliche to suggest this, but Emacs with org-mode and org-roam will do most of what you're wanting. Maybe give https://github

I know it's fast becoming a trope or cliche to suggest this, but Emacs with org-mode and org-roam will do most of what you're wanting. Maybe give https://github.com/susam/emfy https://github.com/susam/emfy a try and see where you get?