Other than the first bullet point in your list[1], my contribution in this regard addresses everything else.

Don't have a link handy but it's on github called "rotsit" (revenge of the something issue Tracker).

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[1] That's the entire point of having the issue tied to a branch: if an issue is marked resolved in the branch you are looking at, then its resolved in the branch you are looking at. Storing the issues independent of branch means you need to also store extra metadat about which branch it is broken on.