Welcome here @tushpat!
Beyond the good advice to not be afraid of down- or upgrading a folder as its relative importance changes, I would emphasise that this:
implies that IDs can cover a lot of ground, too. The point of JD for me is that you can find things in a few steps, because you have an exhaustive and non-ambiguous index to consult at the start. The point is not to overclassify things. If you know how to find your way around your files once you’ve narrowed things down, then you don’t need to do more work arranging things. That’s a waste of time.
I don’t think I would make each class an ID (as I said above). Or even my PhD thesis. I think my ID would contain a list of places to put and retrieve stuff relative to each class or project I was doing. So where is my reference manager, and what are the tags/folders I use for references relating to my thesis.
I think my ID index entry would primarily contain the checklists and procedures I use for staying productive with my thesis work. I would think of this as the place to go to get refocused. What is this project I’m working on, what is my goal, how have I decided I’m going to work on this, what are my study habits, what’s my schedule, where are my tools and resources … Ok, now go do it!
Approaching it this way, the ID would be even broader, like ‘Studying and Researching’ and would therefore outlast my graduate studies. Something like a thesis project is fairly big and messy and constantly changing – lots of drafts and notes – and would live in its own ‘repository’, being indexed in the JDex but not actually stored there. I think in my approach, even my whole record of classes I took would just be a text file in the ID ‘education’. I know many people would give each course an ID, whereas I look for much broader things that feel like they’ll last a long time.
So, maybe giving it its own area or even system actually frees you up to tailor the index you’re creating to fit this currently significant part of your life … as @johnnydecimal has explained, don’t worry about archiving it later being a big step. I know this is sort of contradictory advice to what I said above, but what I said above entails thinking long and hard about how to make categories and areas become as timeless as possible, and if you don’t have time for that now, just give yourself lots of room and burn through those IDs for now, and consolidate them later, because:
It won’t be. But the next reorganisation won’t be a big deal because you’ll be going from one organised state to another.