My thoughts are so all over the place that I've settled on 3x5 note cards. It also makes the transition to the computer much easier, because I can re-arrange them in a way that is somewhat organized before taking a picture that gets transcribed

Possibility to re-arrange is ofc good when working on something in progress.

But how do you archive these cards? That always drove me mad so I use them only for something “encyclopaedical” otherwise it is too much messy.

You might want to check out Scrivener (Mac and Windows). I use that in lieu of note cards. The cork board function lets you re-arrange text and media to your hearts content and then compile the final output to Word, PDF whatever. It's designed for non-linear writing.

https://literatureandlatte.com

The point here is imho that you intentionally remove the computer from the path (in some part of your work) if you want to achieve some focused deep work (in case that you aren’t coding ofc :)