Yeah, sorry, that was intentional, but I didn't realize the links would break. In hindsight, I should have.
Well, it's pretty simple[1], really. I used git fetch upstream to grab all the changes from ar. Then I used git reset --hard to reset my master branch to ar's branch, completely destroying everything on my branch, including commits.
Then I used git push -f to force my changes onto GitHub. Voila, now my fork is in the exact same state as ar. Of course, before I did all that, I created the old branch, so I wouldn't lose my work. Here's roughly what I did:
git branch old
git push origin old
... do stuff ...
git fetch upstream
git reset --hard 2be9ac75f67edfe9b3c43a9515dd78acebba6f1c
git push -f origin
At least, I think that's what I did. I actually had to experiment and mess up some stuff before I figured out how to do it. So my directions may be wrong and you may bork your repo!
But their directions are somewhat different from mine. I don't think I needed git pull for instance, and git push origin :master didn't work for me. So I had to use -f to force the push, since git was kindly telling me that it might destroy my commits (which I wanted to do).
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After using git for a while, I gotta say, I like it a lot more than Mercurial. git gives you the power to do stuff, whereas Mercurial seems to hold your hand a lot more, and say, "no I can't let you do that, Dave"
Now, I'm not saying Mercurial is bad, just that I like the raw power of git, in the same way that I like the raw power of Arc. So for me personally, git seems to be the winner.
It's too bad the links break. But wait, the pull requests' links don't break, because they link directly to the blobs.... I bet the blobs will stick around as long as at least some branch points to them, so playing fast and loose with lots of branch-renaming is only going to hurt tip-of-branch links. Too bad GitHub doesn't have some way to specify redirects (or at least I think it doesn't).