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You should notice a small change to the From address on your email notifications now: they’re no longer from no-reply@github.com. We’re now accepting replies from most email notifications that you’ll…
You should notice a small change to the From address on your email notifications now: they’re no longer from no-reply@github.com.

We’re now accepting replies from most email notifications that you’ll receive:
The biggest change in all this is how these replies are displayed. We figured out early on in testing that we couldn’t expect people to write Markdown. People are going to be dumping code or stacktraces, and will expect them to look nicely. Also, we need to accomodate the various top posters and bottom posters among our users (while holding judgement).

The new email comment formatting still has some quirks, but we think that the power to reply to emails was too much to hold back. Try it out, and let us know in support if you have problems.
A few caveats: