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At Jabref we also looked into this at some point but then decided not to proceed with this due to various issues and limited gains. I also don't know of any high-profile repository that has formalised PR dependencies.
Instead, I would suggest to look for solutions that allow PRs to be merged in a timely manner and where merge conflicts with the main branch are not a big deal.
As suggested in https://github.com/sagemath/publications/pull/142#issuecomment-1259001501 and https://groups.google.com/g/sage-devel/c/hX6ojxlNwOU/m/dup_Ywu1BQAJ, we should add to the transition guide how to model Trac's ticket dependencies in GitHub PRs.
See https://github.com/orgs/community/discussions/4477 for solutions.
Our migration script emits the phrase "Depends on ...", which is used by several solutions (https://www.dpulls.com/ https://github.com/z0al/dependent-issues gregsdennis/dependencies-action#5). This is already documented in the transition guide.
It remains to select one of the solutions and to set up GH Actions workflow.
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