To confirm, no individual file gets a JD number, am I right?
It’s always [Area ID]folder > [Index ID]folder > file?
Where that file is an arbitrary name?
I wondered this, and it seems that when using multiple projects, the full PROJ.AREA.ID numbering is suggested.
I do use the project number in my ID folders, and when I name files.
And…
Within that folder, if I saved an Excel file I would call that file 496.21.11 Whatever descriptive name I’d use.xlsx.
This is important to me, since I plan to utilize J.D for multiple project, but I’m not in love with the idea of numbering individual files.
This is an ‘it depends’.
I find the ID-in-filename really very useful sometimes. Word and Excel docs primarily, at work, so I can scan my recent or currently-open files and immediately see what they relate to. As per the example Jack notes above.
But it’s not mandatory, no. By the time you’re in an ID folder you’re already hyper-organised, you’ve done enough. 
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This is one where you can mix and match. Try it out, see how you feel — changing this particular element of your system is trivial and doesn’t involve re-organising stuff.
So if I want to use ID-in-filename, I would have a folder with AC.ID foldername and within that folder a file with the same AC.ID in the filename, correct? Or do you ever put a file with an AC.ID in the filename in a category folder but not in a Johnny.decimal folder?
This is what I sometimes do, yes. Again, my primary use-case is to see the number in a ‘recently opened’ list, or in the list of currently-open windows (the ‘Window’ menu on Mac, I guess it’s shown on the task bar in Windows?).
I don’t, but only because I never thought of it. @Heloise gets credit for this idea. She came up with a great example: sewing patterns. Her email to me last week, quoted with permission:
Also, sometimes I wonder if, for some categories, it would make sense to have a folder for the category, and then just name the files with the ID number (I barely ever get more than one file in this category, if so they will be named differently and potentially ordered)… but it feels like I might make something explode if I do that?
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So @Heloise, the idea is that instead of having folders under categories, for some instead you just have files labeled with Johnny decimal numbers?
Yep
That’s when most of these folders would only be filled with one file, then it feels like a real waste to put them in folders. When I occasionally have more than one file in there, I’ll just “number” them with b, c, d… as necessary in addition to their JD number