The best learning experiences I've ever made were with the "digital gardening" method explained in the article. Especially the process of writing down what I'm trying to understand and putting it in my own words is hugely beneficial. That old trick of Feynman's where you take a topic you don't understand and explain it to someone – be it a person, your personal wiki or just a text note – really works wonders. And revisiting a note and changing it a bit also seems to reflect how we remember things: Not regurgitating them, but reliving them.
Apart from that I found the process of creating my own personal wiki highly rewarding and can only recommend it to others (if you have the time). It's an absolute joy to use something you've made and explain the creation of it to yourself using it.
In my case I've also made the wiki in such a way that I can add exercises to notes and then do spaced repetition on those (which was also a blast to implement). The exercises themselves can be functions so that things get mixed up from time to time. I don't often do the exercises, but the process of creating them adds another layer of understanding from my experience.
Edit: Continuation...
But this is just me getting excited over the personalized wiki I've created.
The article importantly mentions that "there is no one-size-fits-all app" to best understand something, so it takes some time and experimenting to figure out what works best for you (heck, I think I went through at least 5 iterations of note-making systems before I settled on this one for about two years now). And since we're on HN, I think everybody here has the skills to make their own.
I really wish schools would add a dedicated, mandatory subject about learning to learn. It would have saved me a lot of time I wasted back in Uni and afterwards just trying to figure out how to quell this urge to retain information.