Since I talked about my own derivate of J.D (and P.A.R.A.) last November my implementation underwent some changes recently.
I still use J.D foremost as means to organize notes, nowadays in NotePlan (again). I use it for my files, too, but since I don’t “do” that many (new) files anymore these days it’s a little bit of an “after-use”, albeit a very welcome one.
Initially I simply moved the existing structure and notes back from Agenda to NotePlan more or less 1:1. Of course stuff I had put in a personal and a work “catch-all” logging/journaling category with yearly projects (2021, 2022 etc.) in Agenda plus some other stuff went (back) into the daily notes in NotePlan, freeing up some “J.D space”.
The AC–AC and AC levels originally translated themselves into folders, but where eg. 12/006 Upgrade auf ILIAS 7 was a “project” in Agenda’s terms containing “unnumbered” notes, it now was (and still is) a note in NotePlan. I didn’t feel right to make it a folder because the then unnumbered files therein would become somewhat messy. And a lot of AC.ID folders would have contained only one file. I had already decided to move “sideways” instead in a bit of a “Zettelkasten-inspired” way. If one note (de facto one Markdown file) is not enough (ie. gets too long and unwieldy), it “spawns” linked “sub-notes” with the letters a to z added to the J.D number, eg. (originally) 12/006a File(service)-Migration vs. NetApp-Snapshots, 12/006b Testen des Migrations-Patches etc. These sub-notes do not get entries in the J.D index, by the way.
I (re-)introduced index notes I had already experimented with during my last time in NotePlan (eg. 12/000 Betrieb und Support Index), but that meant putting these on the AC–AC levels (eg. 10–19 Projekte Index) and an Index on the top level (but, ironically, the bottom of the list, because NotePlan sorts folders to the top), too—which completely fell out of the J.D schema (which kept bugging me).
Then I had somewhat of a personal “epiphany”: Why not get rid of the folders (in NotePlan) altogether?
Also I was tempted to try the “classic full-on AC.ID style J.D“.
So after gaming out a new working J.D structure in MindNode (and through some small-scale experimentation directly in NotePlan) I gave up on P.A.R.A. (at least for now) as well as my own three-digit ID schema and folders (and went work on my J.D index before actually moving everything around in NotePlan).
Now in NotePlan (not files!) the only visual structure in the notes site-pane now comes from the J.D notation. Yes, that makes for a very long, “flat” list. I don’t care, though, because I basically don’t use it. I navigate either via NotePlan’s command bar (cmd-j) directly to (or “near”) a specific not (J.D numbers, as we all know, are perfect for that … 
) or simply to the index note (00–09 Index) and “surf” to where I want to go from there. So far seems to work (a lot) better for my brain than a long folder-structured list.
And I’m allowing myself one more deviation from “by the book J.D”: While, when organizing files, I agree that it makes sense for files only ever to live in the AC.ID folders, in NotePlan I don’t have any folders. 11 Betrieb and Konfiguration for example is a note—and so I’m using it as such. Not only does it make more dedicated index notes unnecessary, I’m allowing myself to keep information/note snippets (often no more than a short paragraph or a link) in these notes that would otherwise simply not justify their own fully J.D’d note.
It works surprisingly well for me.
In my J.D index I have an entry 00–09 Index / Organisation und Verwaltung which “translates” just to 00–09 Index in NotePlan (and which will become a directory called 00–09 Organisation und Verwaltung if I ever need it in my files, too) and which serves a my navigational starting point. I also collect links to active projects there:
The name ensures it stays on top of the notes list. The rest of the basically looks like this:
10–19 ILIAS
11 Betrieb und Konfiguration
11.01 Something
11.02 Some Project
11.02a Sub-page
11.02b Another sub-page
…
12 Fehler und Probleme
…
20–29 E-Learning und E-Assessment
…
22 OER und Creative Commons
22.01 H5P
…
etc. pp.
Like I wrote above, everything is a note, the “upper-level” notes serve dual purpose both as indexes and for keeping “small stuff” related to this areas/categories:
(There is nothing special whatsoever about the actual AC.ID notes.)
I moved personal stuff deliberately to 90–99 to leave myself some room for growth for the work stuff (which goes up to 50–59 at the moment).
One thing I like about this implementation: The same J.D index (which, by the way, still lives in an OmniOutliner document) works seamlessly both for the above ”abominable” NotePlan structure (despite my “rule-Breaking” there) as well as—in a very “classic” J.D way—for my files.
And this structure and the dual usage of the ”index-y” notes in NotePlan saves me some J.D numbers. Still, I’m curious how long I’ll be able to make do with two-digit IDs. But thanks to NotePlan keeping its Markdown files accessible via the filesystem I reckon that I can switch back to longer IDs with a bit of BBEdit regexp search and replace “magic” quite easily. Should be doable for the J.D index and the directory names in the filesystem, too. That’s a bridge I’ll cross when the time comes, though.
Lastly: The way I set things up in NotePlan should (for the most part) quite easily be portable to a number of other, similar note-taking apps like Obsidian, Craft etc.
(On the whole nothing innovative, just remixing existing ideas. But maybe it’s still useful to others as a kind of “quarry”.)