I'm definitely in favor of tools on top of my text files. I started with Sublime Text[1] and Markdown Editing[2] Package. I can still and sometimes resort to this setup. I believe that if I can search (Sublime Text is powerful with this) easily, that solves all the connection/relationship between the files.
And a bit of a shameless plug but I have been told by colleagues and friends that my file organizations lasts ages, and are the easiest to navigate. Some have told me, 10-years later, that the system I build and the naming convention are still followed to that day to maintain the software and an easy common-lingual between the designers and developers. :-)
With tools such as Obsidian, it has already shown that this is going to improve as we progress. For me, it is more of the process and patterns of how am I mapping the files/topics/subjects mentally.
1. https://www.sublimetext.com
2. https://sublimetext-markdown.github.io/MarkdownEditing/