I really like the work you’re doing, though it’s heavy for my current needs. We have per-project categories - about 80 of them, at the moment. The group/category management is getting to be a real bear. (On another note, I’d love to see group creation/management optionally bound to category creation/management). About 60% of our categories are private b/c the projects are under NDA.
As you continue your design work, I’d suggest trying some edge case mock ups to see how well they handle large numbers of categories. FWIW, our company worked on over 10k different projects last year. I’ll never agree to support that many categories, but it does make you think about the scalability.