Instead of an overarching project folder, which annoys me by hiding things, I generally have an overarching project that refers to the other projects. In my example above, that would be the "Complete Paper X" project, the one with the two WAITING FOR actions. It's possible that Complete Paper X might _never_ get an actual workable action; it might forever just exist to "wait for" related smaller projects. But by existing, it does link those smaller projects together.
And adding a final action to the smaller projects when those projects are created, something like "Go back to Complete Paper X" adds another backup link. Or, for the example of "Plain this quarter's academic reading" you might have a final action of "Projects X, Y, Q, and R are waiting for this project," reminding you to return and look at all four of those projects. If that extra action seems like clutter, you could instead add the dependency to the project name itself. ("Plan this quarter's academic reading. Needed by X, Y, Q, R.")
Again, this comes from the fact that I dislike nesting and feel that it adds complexity and increases the risk of missing something. I'm sure that many will disagree.
Edited to add: My mind has no problem building a purely mental hierarchical structure from these notes (WAITING FOR, parent project, etc.) on the fly when and only when I need it, and reshuffling these structures based on where I started. A visual reminder of that structure is not only unnecessary for me, but annoying, because the visual reminder can't be easily reshuffled. But I seem to remember reading that programmers tend to be in the ten/fifteen percent of the population that form mental models in one particular way, and the rest of the population forms them differently. The majority way may be aided rather than annoyed by visual hierarchical layouts.
Gardener



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