I love Github issues, it is one of the awesome things at Github IMHO: as simple as possible but actually under the hood pretty full featured.
However one of the things I love more is labels. It is a truly powerful thing to organize issues in a project-specific way. Unfortunately if an issue is a pull request, no labels can be attached. I wonder why.
Also I would love the ability to merge against multiple branches instead of the taget one, directly from the web UI.
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