feat(cos): heal zombie issues — partial-ship hybrid + issue-reconcile task

[atomantic]

Problem

A partially-completed issue became an un-claimable zombie: OPEN + in-progress + assigned, with its PR already merged. The claim queue treats in-progress as "claimed and being worked" and skips it, so the remaining scope is never re-picked and never finished. Live examples caught in the wild: #2220, #2179, #2175 (all healed by hand as part of this work — #2220 closed with follow-up #2241 filed; #2179/#2175 released for re-claim).

Root cause: the completion flow had no partial completion state. /do:next Phase 7 was binary (fully-done → close + unlabel), and the branch reconciler is branch-centric so it never touched the linked issue.

Fix (agent-judged hybrid, applied in two places)

Part A — teach the claim flow to partial-ship (claim-issue / -gitlab / -jira):

• Phase 5 chooses the PR trailer deliberately — Closes #N for a full ship, Refs #N + a ## Remaining section for a partial one.
• Phase 7 reconciles the issue: separable remainder → close + file a scoped plan follow-up (Refs #orig); continuation → keep open, post Done ✓ / Remaining ▢, remove in-progress + assignee so the queue re-picks it. JIRA records remaining scope + files a follow-up ticket.
• Prompt-version discipline: claim-issue 3→4, -gitlab 2→3, -jira 1→2; outgoing bodies preserved verbatim in PREVIOUS_DEFAULT_PROMPTS; integrity snapshot regenerated.

Part B — new issue-reconcile per-app CoS task (sibling to branch-reconcile, disabled by default):

• server/services/issueReconcile.js — pure classifier + gh/git gatherers. A ZOMBIE is open + in-progress with a linked merged PR and no live claim anywhere (no open PR, no local/remote/CoS claim branch, no active agent). Boundary-safe ref/#num matching (issue-222 never matches inside issue-2220).
• Deterministic pre-step + dispatch block in cosTaskGenerator.js, parallel to branch-reconcile — perpetual drain with a zombieSignature convergence guard; parks when clean.
• autoClose toggle (ON default; OFF ⇒ comment + release only). Coordinator dedupes follow-ups via a Refs #orig search so federated peers can't file duplicates.
• Registered across taskSchedule (interval + MANAGED_AGENT_OPTIONS + description), versions.js, cosValidation allowlist, and the coordinator prompt.

v1 zombie scan is GitHub-only (parks on non-GitHub apps); GitLab/JIRA siblings deferred.

Tests

• server/services/issueReconcile.test.js — 30 new unit tests (ref/reference matchers, ZOMBIE/LIVE/STALLED classifier, end-to-end reconcile over mocked gh+git, signature, prompt formatting).
• Full server suite green: 16,859 passed, 20 DB suites skipped. Integrity-snapshot test confirms the prompt-upgrade contract (outgoing bodies preserved, versions bumped).

Design record: docs/plans/2026-07-06-issue-reconcile.md.

https://claude.ai/code/session_013EZAPV4vq8A1ea6TB45kXq