Stack split across merge groups closes the pull request at the boundary instead of continuing it in the next group

gh stack merge の実装とその merge queue の処理から始め、merge group がブランチを削除したときにトリガーされる REST/GraphQL の更新を追跡します。delete_branch_on_merge を有効にした 5 つの PR の stack を再現します。完了条件は、境界の PR がオープンのまま stack base をターゲットに再設定されるか、stack を失わずに次のグループで継続されることです。

Summary

When a stack is split across consecutive merge groups, the pull request at the
split boundary is closed instead of continuing in the next group. Its base
branch (the head branch of the last PR in the merged group) is deleted by the
merge, GitHub re-targets the PR one link up the chain — onto the base's base,
which the same merge also deleted — and then closes it because that branch no
longer exists.

The stack never finishes landing, and the closed PR cannot be recovered through
the API or the UI: each obvious route is refused by a different validation (see
Impact). Recovery required force-pushing two deleted refs back to the remote.

Observed twice in the same stack, ~50 minutes apart, with gh stack v0.1.0.

Pull requests are referred to below as PR A … PR E on branches a … e;
timings, error strings, configuration values and documentation quotes are
verbatim from the real occurrences.

Environment

• gh stack v0.1.0
• Base branch main uses a merge queue:
  mergeMethod=SQUASH, mergingStrategy=ALLGREEN,
  maximumEntriesToBuild=8, maximumEntriesToMerge=5, minimumEntriesToMerge=1
• Repository settings: delete_branch_on_merge: true,
  squash_merge_commit_message: PR_BODY
• No ruleset on the base branch — GET /repos/{owner}/{repo}/rules/branches/main
  returns [], so require_last_push_approval and dismiss_stale_reviews_on_push
  are both off. This distinguishes this report from #174 and #323, where
  invalidated latest-push approval is the stated mechanism. Every PR here kept
  reviewDecision: APPROVED throughout, including across force-pushes.
• All PRs APPROVED, MERGEABLE, required checks green when enqueued.
• Every pull request in the stack was in the queue and building concurrently
  when the merge happened — added_to_merge_queue is recorded for all of them at
  the same second, and none was ejected before the merge. The stack was not too
  large for the group either: in the second occurrence it was 5 pull requests
  against maximumEntriesToMerge=5, so the documented 50-percent buffer was not
  even needed. Only the first three merged.

Reproduction

1. Create a 5-PR stack: main <- a (PR A) <- b (PR B) <- c (PR C) <- d (PR D) <- e (PR E).
2. Merge the whole stack (gh stack merge --yes). All five enter the queue
   together — every PR records added_to_merge_queue at the same second — and
   all five build concurrently (maximumEntriesToBuild=8).
3. The queue merges only PR A, PR B, PR C, while PR D and PR E are
   still in the queue.

Actual

T+0s   PR A, PR B, PR C   merged                     (all three, same second)
T+2s   PR D               base_ref_deleted
T+2s   PR D               closed
T+2s   PR E               removed_from_merge_queue   (actor: github-merge-queue[bot])

• PR D's base was c. After the merge it reads b — the base of its base,
  deleted in the same operation — and the PR is closed.
• PR E being ejected is expected and documented; it stays open because its own
  base branch d still exists.
• The remainder of the stack does not continue in a subsequent merge group. It
  cannot: the PR at the boundary is closed.
• Why the queue stopped after three is unexplained by any configuration value —
  all five were enqueued and building, and five is within
  maximumEntriesToMerge. Whatever the reason for the boundary, the failure
  reported here is what happens at it.

The first occurrence was identical with an 8-PR stack: three merged, the fourth
closed 2 seconds later, the rest left open.

Expected

Three documentation statements describe what should happen, and the observed
behavior contradicts the first two:

A large stack may also split across consecutive merge groups: the merge queue
allows a merge group to exceed its configured maximum size by up to 50 percent
to keep a stack together, and any pull requests that don't fit continue in
subsequent groups until the full stack has landed.

— Troubleshooting stacked pull requests

Merge part of the stack by merging a mid-stack pull request. The pull requests
below it merge too, and the pull requests above stay open and automatically
re-target the stack's base branch.

— About stacked pull requests

Stacks are kept together in the merge queue. If a pull request is removed or
ejected from the queue, all pull requests above it in the stack are also
ejected and removed.

— Troubleshooting stacked pull requests (this part works as documented)

So the PR at a group boundary should either continue in the next group, or at
minimum stay open re-targeted to the stack's base branch. Re-targeting to
the immediate parent's base is only safe when that branch still exists, which it
never does when the stack is merged as a unit with delete_branch_on_merge
enabled.

Any of these would fix it: re-target survivors to the stack's base rather than
one link up; re-target before deleting merged head branches; or skip head-branch
deletion for a branch that is the base of an open stacked pull request.

Impact: the closed pull request cannot be recovered

Four recovery routes, each refused by a different validation:

PATCH /repos/{owner}/{repo}/pulls/{D}  base=main state=open
  422  Cannot change the base branch because the pull request is part of a stack.

PATCH /repos/{owner}/{repo}/pulls/{D}  state=open
  422  state cannot be changed. The b branch has been deleted.

# after `gh stack unstack <stack>` lifted the stack restriction:
PATCH /repos/{owner}/{repo}/pulls/{D}  base=main state=open
  422  Cannot change the base branch of a closed pull request.

# and where the head had been force-pushed after closing (e.g. by `gh stack sync`):
PATCH /repos/{owner}/{repo}/pulls/{D}  state=open
  422  state cannot be changed. The d branch was force-pushed or recreated.

Changing the base requires the PR to be open; reopening requires the base branch
to exist; and reopening also requires the head to be at the SHA recorded when the
PR closed. With the base branch deleted, there is no ordering of these calls that
succeeds.

Recovery that worked

1. git push origin <sha of b>:refs/heads/b — restore the deleted base branch.
   The SHA survives only in refs/pull/{B}/head.
2. Where the head had moved since closing, rewind it to the recorded
   headRefOid (also recoverable from refs/pull/{D}/head).
3. PATCH /pulls/{D} state=open — now permitted.
4. gh stack unstack <stack> — required before the base can be changed.
5. PATCH /pulls/{D} base=main.
6. Restore the real head, delete the scaffold branch, and gh stack link to
   rebuild the stack.

A user who did not know the SHAs live in refs/pull/{n}/head would have to
abandon the pull request and open a new one, losing its review history.

Notes

• gh stack merge --help says that under a merge queue the pull requests "are
  added to the queue together but merge as the queue processes them, so they may
  land in separate groups rather than all at once", while Merging stacked pull
  requests describes the selected PR and everything below it landing "together
  as a single operation". Both can be true, but with delete_branch_on_merge
  enabled the first has a consequence the docs don't mention: any group boundary
  inside a stack closes the pull request at that boundary.
• gh stack unstack <stack> reported
  ⚠ Some pull requests are queued for merge or have auto-merge enabled while no
  pull request had either — that is #372.
• gh stack view --json reported the closed pull request as "state": "OPEN",
  so neither view nor --short surfaced the closure; only the REST/GraphQL API
  showed CLOSED. Filing separately.