Stale or missing refs/pull/N/merge on stacked PRs silently prevents all pull_request workflows from running #319

What happened

Three PRs in a 10-PR stack stopped running CI entirely. Not failing, not skipped: the check runs simply never get created, so the PRs look like CI has not started yet and stay that way indefinitely. pull_request_target workflows keep running on every push, which makes the PRs look half-alive and hides the problem.

The common factor is refs/pull/N/merge. pull_request workflows run against that ref, and on the affected PRs it is either missing or pinned to superseded commits:

PR C  merge ref parents: 46c51a0a7  e1ca4188f   <- both superseded
      actual base/head:  eb03b5605  6bc00ac9c

PR D  merge ref parents: e1ca4188f  d90f608e5   <- both superseded
      actual base/head:  6bc00ac9c  f8dbef22c

B, C and D each have a head that is a strict descendant of its base, so merging is a fast-forward and git merge-tree reports zero conflicts. The CONFLICTING state is phantom, and appears to be the same stale merge computation (see discussion #229).

The code and the runners are both fine: a pull_request_target labeler ran on every SHA, and workflow_dispatch runs of the same three workflows against the same branches all pass. It is specifically the merge-ref-backed pull_request path that is dead.

The failure is silent. A red X is actionable, but an empty check list is indistinguishable from "queued", so a PR can sit for days appearing to wait on CI when nothing will ever run. We only found it by comparing check-run names across sibling PRs in the same stack. Any repo with required status checks would block forever with no indication why.

Expected

Either the merge ref is recomputed on push so pull_request workflows run, or the PR surfaces that its merge state is stale instead of rendering an empty check list.

Recovery attempts, all blocked

• Pushing new commits, five times, no recompute
• Close and reopen, which deleted the merge ref instead of rebuilding it
• Retarget the base away and back: 422 Cannot change the base branch because the pull request is part of a stack
• gh stack unstack: Unstacking not allowed: Pull requests ... cannot be removed from this stack, naming the 13 merged members

Stack membership blocks the base fix, and merged members block removing membership, so there is no way out from the client side.

Environment

gh 2.68.1, gh stack v0.0.8. A stack of 10 open PRs on top of 13 merged ones, trunk dev.