I am wondering how other people handle their JD folders across different filing systems. For example I keep the bulk of my personal notes in Obsidian; but, I also keep some in Notes.app (I have my reasons). I also have files in iCloud Drive (personal), OneDrive (work), Dropbox (work), and Zotero that I want to keep organized. What I am finding, though, is that I have several empty folders depending on the types of data and the location where that data lives.
Here’s an example.
- 30 Career
- 31 Job Search
- 31.01 Application Materials
- 31.02 Accomplishments
- 31.03 Resources
31.01 Application Materials Contains 1 item in Notes.app, 0 items in Obsidian, and a whole bunch of items in iCloud Drive. There reverse is true for some other folders, where most of, if not all of the data is in Obsidian or Notes.app and not in iCloud. Is there some way that I am missing to avoid having these empty folders? It just seems like a waste. It’s also becoming difficult to keep track of which IDs are used. If I want to make a change to the organization, I have to go make the change in all of these places. Has anyone tried using divergent number systems based on the filing system they are using for that data?
I like the JD system a lot. I like being able to think, “10=personal, 30=carreer, etc.” I love the way it works using Alfred. So, I want to make it work for me.
I would appreciate any wisdom or suggestions.
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The answer is right here: Tracking your numbers | Johnny•Decimal
Don’t worry, I kind of over-read it the first time, too. 
In short: Keep a central index.
That’s it, really.
You don’t have to and probably should not create empty folders/notes/whatever where you don’t need them. All your J.D numbers live in your index (and all of them probably live only there), along with a location (or several ones). And, yes, at least for me that means I (usually) create a new entry (anywhere) by creating it in the index first. So you’ll end up with gaps at the different locations. That normal.
Also it actually does not matter where you keep your index, I believe. Use what suits you best. I’ve personally experimented with Numbers and different outliners (especially OmniOutliner, MindNode and Zavala), but these days I just use a simple Markdown outline like this:
# 01.01 My J.D Index
## 10-19 Area
### 11 Category
- 11.01 Something
> Location(s): Things, Documents
- 11.02 Something else
> Localtion(s): Ulysses
etc. pp.
And, yes, the J.D index has its place the the J.D index, too. 
(Also see eg. My derivate of J.D (and P.A.R.A.) and Using an outliner for the index among other threads here.)
PS: Don’t diss Apple Notes—it has become quite capable nowadays! 
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OK. This makes a lot of sense. It was the locations part that made it click for me. Thank you!
This was frustrating me, too, and I knew about the index note idea, but it seemed like yet another separate thing to update (and which could easily fall out of sync with my actual files), so I never really did it.
I did the thing you’re not supposed to do, which is to treat my folders in Dropbox like the index. My Obsidian vault now wraps around my whole JD system (which actually works better than I thought it would, with many folders excluded from syncing). In Zotero, there are some things replicated (folders related to academic publications or classes I’m teaching), and they get the relevant number prepended, mostly so I keep seeing them and remember what the numbers are (which I still don’t really). In Things, I replicate the top-level areas from JD as areas of responsibility, and some projects end up with JD IDs on them (this is the loosest part of the system now, but I’ve been using Things forever, so it’s been a slow process integrating JD in there).
Not a solution for your problem at all since I really have tried to keep only one note system and one file system, but I figured it was worth having here on the thread. (At the very least, it seems like your file storage may correspond to different areas in your JD system? So you could know that 30 lives in OneDrive, etc., and avoid conflicts that way. It sort of depends what your reasons are for maintaining separate notes/files; if those end up corresponding to areas, then you wouldn’t have much issue with conflicts. If you find a lot of crossover at various levels, that might also be a sign that there’s a more organic way to sort your system so that the tools you use do deal with mutually exclusive areas?)
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So I do:
Cloud storage 00.00
Evernote 00.000
That way don’t have to look for what is the next number on a separate number tracker list.
Could you explain this more? I don’t understand exactly what you mean. Are you keeping your tracking list in those locations? If so, how do you keep them in sync?
Let’s say 10 Personal
iCloud files would be 10.01, 10.02, etc
Evernote would be 10.001, 10.002, etc
The .01 or .001 is so I don’t have to go back and forth to see what number is next.
Just reviewing old forum posts as I re-write the site and noticed this little comment. Yes! My index is always 00.00, it’s at the very top of the JD tree.