I‘ve been experimenting with J.D myself for a bit now, first in NotePlan (where something like this maybe is a bit more essential because of its (from an Agenda point of view) different way of organizing note/files/projects it its sidebar) and now in Agenda.
I‘m actually in the process of moving everything (back) into Agenda after a having used NotePlan for a few months—and now hoping to finally ”settle down” in the former for the long haul. (Both apps are good, are well-made, have their strengths and weaknesses and actually different way of working despite a _superficially _similar “core concept”—but what drove me to Agenda in the end, was among other aspects it’s a bit greater polish, no plugins (!), no themes (!), more “Things-like” approach. But I digress …)
Still, Eduard has some interesting ideas he also blogs a about and after initially dismissing P.A.R.A. (as “simply not for me”—after coming from and probably still kind of thinking in Things, where for me it would have felt absurd not to put projects under the areas …), his personal combination of PARA and J.D got me thinking.
In the end I realized that I, of course, do not have to adopt systems like these completely, but (Duh, I know! 
) can just treat them as kind of toolboxes from which I may take just what I need and recombine and modify it to my personal needs. (In that I am probably not yet at the end of my journey but since I kicked off this thread I kind of felt obliged to contribute, too. 
)
So right now I’m rolling my own combined adoption of both PARA and J.D.
PARA kind of turned into PARP—projects, areas, resources, personal. I wanted to separate personal stuff from work stuff, but get away from a binary work/personal top-level. And of course (?) “work” is far more extensive, so it kind of takes the lead.
(Inspired by Agenda) I’m envisioning a more “in-place” approach for archiving files, too, but anI haven’t gotten around to reorganizing those, yet, as most of my work tends to produce very few (local) files anymore these days (which was the case even before NotePlan/Agenda times, when I used mostly Things and (mostly) Ulysses for quite a long time). So the clear focus is on Agenda right now. And I’m still not sure how much overlap between files and Agenda I should try to enforce—and whether that is actually of much importance beyond a more theoretical realm.
As for J.D, since the actual projects live relatively far down in the (albeit quite flat) hierarchy I’ve decided to give myself a little bit more leeway on the ID-side. If this really pans out, 99 (smallish!) projects/“projectlings” is not a lot, not even (unevenly distributed) over at the moment four categories. So I’ve come up with a “12/001” etc. schema instead of the “classical” (recommended by Johnny) “12.01” schema. I also dismissed the . as a separator because I live in one of those parts of the world that use it as a thousands separator—and so “12.001” would just look too much like a number (ie. “12,000”).
Anyway, so far so good. I’m curious as to where all this will lead me. 