Posting on behalf of @cls whose Discourse is being a little odd.
New user question. Is it correct that if one selects the “Method 1: Individual notes, one per index entry” under index creation, then there would not be a separate single file master index (.txt or .md) as well (under 00-09 system management)? If so, it would necessitate inefficiently having to change two things in the event a category would be added or altered. Thanks!
And I’ll reply as me. 
Correct: if you have one-note-per-ID (which I recommend and use myself), you do not also have a master note at 00.00.
@johnnydecimal with Obsidian you could use datavies to query all index notes to make an automatic master note.
Yes thanks - I had previously downloaded that from dataview example from github and played with it. Worked great [Of course, that behavior created the underlying problem - bear, apple notes, devonthink, craft, notion, etc, etc].
Also, if the notes in bear constitute the jdex, should you have hundreds of other notes in bear as well (even if appropriately numbered), since it is much less ‘clean’?
My preferences here show that I’m not a massive note-taker: my notes are just in the ID files themselves.
Otherwise this is where the + syntax from extend the end works well. Every sub-note related to an ID can be called 11.11+ Whatever you want to call the note.
The Obsidian users amongst us do this differently: some tend to prefer JDex entries to be their own separate thing, distinct from the rest of their notes.
Hold on! My understanding was that before you go anywhere, when starting work, you go to the Master Note at 00.00 and open it up and always find the place there to add any new entries?
One or the other. You either have:
00.00 that contains a list of all of your IDs, orI prefer 2.
Can you do both? Make a master note, linking to all the sub notes. That way you have the massive overview, but also the ID notes. It’s only a little extra overhead to add the ID to the top-note.
Yeah you could. I dunno though, that middle pane of Bear is a list of all your notes. I’m not sure there’s much benefit to re-creating that in a note.
If you do do this, use [[wiki-links]] for much speed.