I resolved the index issue the one note per id way. I started with a single dedicated index note, but that means doing all things twice.
Ultimately, I’ve resolved using my notes as my filesystem.
All i have are JD notes inside Joplin (but Obsidian would work also), and any file that is not raw text, is attached/embedded inside one note with the ID. That way everything is under an ID (wich is the purpose of J.D).
Then the whole notes program is synched. (so when i sync notes between devices, im also synching files)
So instead of having a real folder structure, its all “virtualized” inside the notes app.
Here is an example i did for a work project, this one is abandoned as i changed to another job position, but the same idea (all files inside joplin) is what i use for my personal data still today