Interesting. Interviewee can't use GitHub for their class because the servers probably are in the US: "Copyright is a big issue. For instance, we are working with a novel. In Canada, that novel is in public domain so it can be accessed online, but not in United States."
Looking at the challenges, it would be cool if GitHub picked that up and published best practice guides for teachers and also collaborating researchers. Such guides could come from this study and others like it. I remember they're doing research on how researchers use GitHub already.
I use GitHub's gollum  git-based markdown-supporting Wiki for pretty much this. It's easy to add a basic username / password protection. I run it on a Digital Ocean instance that had some capacity left over and have a cronjob push to a private bitbucket repo every 30 minutes for backup. I don't have to create notebooks and can use GitHub-flavored markdown (or other any syntax gollum supports).
That said, I like basic idea of extending magpie with a PDF scraper and email. Maybe it would spare some energy to fork gollum and add extension to it to make it more Evernote-like?
Right, it didn't turn up in the exploratory survey or in the interviews. Well, also we wanted to know how developers use Twitter ... the API I guess wasn't that important at least to the people we talked to. Some said in the initial survey that they had switched to App.net though, but it was only a tiny fraction that we weren't able to talk to. As we say in our study, our results are not generalizable, so there may still be several other issues lurking that we didn't catch in this study.
Then again, RSS is how "tech savvy" (incl developers) would use twitter. Sorry I digress, maybe I do take RSS too seriously. But for me it is really important to draw a distinction in how a service is consumed. Using a website often means the possibility of being unconsciously engaged, thus spending there more than the desired time.
Well, most of the developers we talked to were professional developers, so they probably were tech-savvy. Maybe the removal of RSS happened so long ago that nobody's really frustrated by it anymore -- either you use a client (CLI if you want, "t" is neat) or you move on to something else?