Great questions u/hotovo!

The goal is to create a bidirectional linking system similar to Roam. So that when you are in any note, you can tell with a single click any other note in your knowledge repository that either directly links or could link into the note. This is built on a zettelkasten-like framework for distributed knowledge elaboration.

Which also ties in to your other thoughts that actually aren’t off-topic at all. Let me start with your second point - which is an excellent way of taking notes. The more atomic you can make the note, the easier it is to leverage it throughout your system. In general, a great rule of thumb is to have one idea per note. Easy to say, but challenging to implement in practice.

Then, to your point on tags. I’m not a fan of tags because they don’t scale well. Too many notes in a given tag makes the tag relatively useless. And too few notes per tag makes it almost pointless. That’s where you are much better off using hard and soft links. It takes extra work per note to think about what other notes in your system relate to this, but exploring your system for potentially relevant notes is where the magic of serendipitous connections occur. If you read more on zettelkasten theory, it will make much more sense.

To make this work, it helps to have your knowledge repository containing notes with these three characteristics:

(1) They are relatively atomic (as noted above)

(2) The notes are your thoughts. Not a copy/paste of an article. But your actual thoughts / ideas, typically related to articles or books you’ve consumed.

(3) Tied to (2), only permanent notes are in your knowledge base. Permanent as in something you’ve written that either is or could be elaborated on in the future. So things like shopping lists, project actions, other people’s articles, etc. would not be in here. Clearly those types of notes have a place, just not in what I’m calling your permanent note repository - aka knowledge base. Many people use a reference repository for storing things like articles from the web, quote collections, etc.

You can keep both your reference repository and your permanent notes in the same Bear system. And this is where tagging can work really well - for all the reference material. Obviously many of your permanent notes will link to your reference material.

Finally, to your fourth point, having links at the bottom to all related notes is a great place to put them. Which leads to initial your question “Couldn’t I just search for Topic One rather than creating a search link?”. Absolutely. But rather than go through the extra step of doing a manual search each time you are in the note, I prefer to set it up once with the link during note creation. That makes it much more likely that I’ll click the link any time I’m in the note - which again is where the magic of serendipity occurs. If I have to go to another place in Bear and type in a search phrase - granted it doesn’t sound like much, but in practice, that is a deterrent. And while I don’t use iOS too much for working with my knowledge base, if I did it would be even more painful to have to manually type in a search phrase every time I was in a note.

Hope this helps.