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How does it handle things like `git rebase -x

It currently doesn't; `jj run` is a command to do this, separate from rebase, which has a PR open but hasn't been merged yet.

There's also no examples for how you work out which commit has a conflict marker

Every bit of UI shows a bright red (conflict) on conflicted changes, it's hard to miss.

And I imagine it all breaks in colocated repos too

It doesn't break in colocated repos in the sense that the feature works when you're working with jj, but you'd want to update your submodules and use gh cli on non-conflicted things.

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