I see your point, and quite frankly, I also understood the benefit of the brain way.
However, for some of us, our brain thoughts are everywhere, and it’s more difficult for those with ADHD because they are already struggling to sort out data in their brain in a hierarchy.
In a study, on brains of ADHD vs normal brains, found that individuals with ADHD show alterations in blood flow to various brain regions, including decreased flow to prefrontal areas, which suggests decreased brain activity. The prefrontal area is responsible for many important tasks, such as executive functions like planning, organising, attention, memory and emotional reactions. If anything - having a clear structure and an assistive visual tool to sort things out really helps those (with ADHD or not) who face similar things as mentioned above. By no means are these considered disadvantages, but it’s worth considering methods to approach things like organisation, planning etc.
I’d prefer the combination of both: tree/hierarchy view, and then you can tag these docs with a tag on some parts of the doc (like tag the H1 title or paragraph with #some-topics), and in the tree view, it will link all the documents that have the tag, but also based on hierarchy. Because actually everything can be related, that’s why it’ll be messy and confusing. For example, the basic concepts of JS include Variables, Data Types, Operators, Expressions, Statements, Loops, Functions, Arrays; all of them are connected somehow, i.e. template literals (best explained in variables but also in expression topic). However, if you’re sharing these notes or re-reading them again after a period of time, hierarchy is good to tell you when to know this (so you don’t suddenly read some advanced topics before you are ready). This is when tags become handy - that leads to the network diagram. But the tree structure must not ever be ignored too.
It’s like playing an RPG game where you progress through the levels and unlocks more skills and abilities. Then you will know how to use them properly, when to apply them, is able to activate them anywhere, in any order you want.
As I mentioned earlier in my original post, my brain already works like the diagram you mentioned, it’s a lot to process, and I like it the way it is, but I sort them out with tree structure. I do not need my digital notes to enforce the brain way again, where it became very restrictive and overwhelming. I didn’t quite use any digital note-taking like Notion before during my PhD (regrettably), yet I use physical notes. However, when I started working, running my company and learning coding topics, I found the dire need to organise things, and I began to appreciate it more when I could.
Scientists, thinkers, etc, throughout history, rely upon this traditional method and that’s the pillar of how our civilisation progresses. I am hardly convinced of the need to reinvent the wheel or method; rather the modern way (i.e. the brain way), if anything, can augment this traditional method and increase its efficiency, not replace them completely.
An interesting and similar approach is made by Trilium: GitHub - zadam/trilium: Build your personal knowledge base with Trilium Notes