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I don't agree that in all cases the Misc/NEWS entry and the checkin comment must be wholly different. While I concur that that's called for now and again, I believe this to be rare. Most checkins are small changes, and a single-line summary for both Misc/NEWS and the first line of the checkin comment will suffice.
However, clearly the tool should *support* making them wholly separate. But that's easy to support. pyci now supports a "-n" or "--newsonly" flag, which instructs it to only add the Misc/NEWS item and to not check in. This is presumably also nicer for folks used to shell-integrated hg tools (TortoiseHG etc).
I think it's important that this *not* be the default behavior, as it's going to be hard enough to get the core dev community to adopt this tool, and I would prefer it make the experience nicer rather than clunkier.