For me, it depends what sort of things I'm taking notes of. I use the default Notes app on my mac/iphone if it's something that I would like to remind myself of, things that I keep track in this app are:
When studying I usually have an old squared pages notebook on my desk. I use it for scribbling things, taking notes of things I am studying, draw schematics to implement code... pretty much anything.
Then, when I want to make sure that I know something I get this old notebook and pass the contents into a blank paper and add it to a folder where I keep all the things I should know/learn.
Finally, if the thing I'm learning it's very code intensive I usually keep a digital file in my documents folder (I back it up to the cloud and an external drive regularly).
This might not be very efficient though but I seem to know where is what all the time haha
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