◇ Could this help me?
Yes on the structural point, no on the blanket dismissal. The real insight is a good one: if the goal is for an agent to execute work, plain files in a working directory beat a note application, because the agent can read, write, and run things in place instead of chatting about them. The framing that note-taking apps are worthless does not hold, since capture, linking, and retrieval are genuinely different jobs from execution, and plenty of people need the first without needing the second. Take the folder-based execution system and skip the argument that the alternative is a waste of time. This is a general practice.
I want a working system rather than a notes archive. Set up a folder structure in a working directory where an assistant can actually operate: separate areas for raw capture, active projects, reference material, and outputs, with a short instructions file at the root explaining what belongs where and how a new item should be filed. Then show me, with one real example, how a request would flow through it from capture to finished output.