@viv @oranga
I’ve more or less combined everything now that obsidian mobile exists and I use syncthing. Here’s my current layout:

all of these folders are my obsidian vault. I’ve split out a second one for just handling the 10k notes from zotero alone because it got cluttered but I’m thinking about ways of combining them in again
Everything below the 100 level is subcategorized into 10’s and 1’s, if necessary. Each of these areas uses a slightlly different system (Cutter Classification, Johnny Decimal, etc)
For example, here is 400, using cutter classification.

Zotero has exactly similar categorization, and that is because it makes no sense to store 5k PDFs on a mobile phone. Class&UBC on Zotero just holds PDFs that I’ve read for class.
@trubes – what sort of level of complexity are you looking for?
I might recommend