If you deem .org to be sufficient and want to use Emacs¹ itself, there is an extension for the zettelkasten method of note taking that you might find useful.

1: Despite originating with the Emacs community, .org files are recognized by many (most?) IDEs, but I’m not sure if extensions are regularly ported to non-Lisp editors.

This is a mandatory comment about Emacs’ org mode since .org files are extremely similar in syntax to .md and can be interconverted extremely easily.

Lazily reasoned misanthropic nonsense, if every scientist were of this zero-sum mindset they’d all have long since transitioned to industry roles in engineering for the higher average pay alone.