Those are both things that would likely fall in this repo, even if only as tracking upstream dependencies for an enhancement.
Here's a rough cut of what I'm thinking at this point for the repo. We'd use issues to track various different items based on label categories. Any artifacts would be tracked in folders:
|-- Current minimum accepted for milestone
|-- test plans/
|-- Atomic Host Definition
|-- Benevolent Dictators - the deciderers
|-- Roadmap (?)
|-- README.md - how to use this repo
architecture - (don't like the name)
tools - tooling
docs - documentation problems
ecosystem - Fedora / CentOS specific
delivery - shipping issues (vagrant support, local compose)
upstream - issue with upstream package
Collections of issues
So for the flannel docker-opts, I can see that as an issue with a 'why this impacts Atomic' labeled as flannel, blocker, upstream, enhancement. This could also be referenced by a larger issue tracker 'Add Flannel' that used the GitHub markdown checklists.
Something like this tracker issue (though I don't know why they didn't use a Milestone here)
Am I off base here?