Essentially time passing is a common thing for anything, all of the rest quickly became dirty or at least have some dirty dump of information here and there. Long story short it's a nice potential continuation of the experiment start taking notes in timeline, storing files in timeline and figure out how to make "dynamic hierarchies" that works well in this model.
I've done something myself with Emacs/org-mode/org-roam notes, with kind-of daily notes and file attachments, it's not perfect nor general but scale a bit. A filesystem approach it's uncharted but seems to be equally possible.