When I was doing my PhD I ended up putting all my development into one repo and all my documents in a second because of GitHub's per repo rules. I didn't know about an academic pricing (they might have had it, but I think it was added after I finished) and I asked about the rules because I wanted a number of small repos, but all told would only be a few hundred meg at most. I was told no, so I decided on the two repo strategy. It worked, but it was awkward.