Proxying to a server is annoying and ugly (and requires an always on connection to do anything substantial), and loading from the local filesystem is slow, complicated, and difficult to use and re-save. But I think there could be a really powerful way of solving this problem that I haven't seen mentioned anywhere else.
Work directly from a hosted git repo over HTTPS.
It would require a re-implementation of a subset of git in javascript, but from there you could plug it into the BrowserFS as a backing store, and you could then work directly from a git repo (and not just from a "blessed" git backend, but from any git backend that provides "git-over-https"). Loading files from there, saving them locally in indexeddb or something, then committing them back to the repo when ready.
I've only given this a minute or so of thought, so please tell me if i'm missing something big here.
Edit:
Giving it a little bit more time, it looks like a js reimplementation of enough of git for my uses already exists [0], and there seem to be at least 3 others as well. But in the notes he mentions that CORS is not and most likely won't be enabled for github which could be a problem. However that's not really a technical problem but more of a "political" one. If something like this became popular and perhaps other hosted git solutions (like GitLab) decided to allow you to enable CORS per account or repo or something, it could light a fire under GitHub's ass to allow it.