I started working on this a few weeks ago:
https://github.com/trane-project/trane-math It currently needs a README, but you could take a look at the courses on how I am building the flashcards. It's easy to reference external resources, so that's what I have been doing, rather than trying to create exercises of my own.
I am starting with a very basic olympiad-style book and a book based on Euclid's Elements, because I don't have the understanding required to clearly work out the dependencies of more advanced stuff. And I also would like to start at the beginning to make sure I don't miss anything.
The ideal end state is to have courses that cover all the undergrad and grad math curriculum. I am also curious on whether this could be used by researchers to keep up to date with the latest research on their fields. But all of that is a long way out.
As for your question, there are a couple of ways that Trane could handle multiple paths through similar material.
1. Just have separate curriculums. You could copy the courses, but the second copy has different dependencies, courses/lessons IDs. For example, one could have a series of courses teaching the undergrad MIT math curriculum and another the Harvard curriculum. They might share a lot of the material, but the order will be different.
2. Trane does not lock you into a specific order. There are filters that let you specify which parts of the graph you want to study. You are free to get questions from specific courses and lessons. You can also use the metadata in the courses to say things like "give me questions from all lessons teaching linear algebra" or "give me questions from all courses on real analysis but not from the lessons on set theory". The dependencies between the lessons that match that metadata are still respected. There are a few more options, but you get my point. The dependencies are not set in stone, and there's freedom to jump around and study specific topics.
I actually use option 2 most days. If I want to practice guitar, I just set a filter to give me exercises from the guitar. Similar thing when I want to practice the saxophone.