bd sync: update issues.jsonl after deacon kernel epic

.beads/issues.jsonl

@@ -333,6 +333,7 @@
 {"id":"gt-ouo","title":"gt swarm start: Does not spawn polecat sessions","description":"gt swarm start marks swarm as 'active' but doesn't start any polecat sessions.\n\nRepro:\n1. gt swarm create gastown --epic gt-hw6 --worker Toast --worker Nux\n2. gt swarm start gt-hw6\n3. gt session list - shows no new sessions\n\nExpected: Polecat sessions should start for each worker.\nActual: No sessions started, workers sit idle.","status":"closed","issue_type":"bug","created_at":"2025-12-17T22:25:43.430981-08:00","updated_at":"2025-12-17T22:31:58.849531-08:00","closed_at":"2025-12-17T22:31:58.849531-08:00"}
 {"id":"gt-ov2","title":"Refinery agent: merge queue processing loop","description":"The Refinery agent processes the merge queue, merging polecat work to main.\n\n## Interface\n\n```go\ntype Refinery struct {\n    rig    *Rig\n    queue  *MergeQueue\n    git    *Git\n    mail   *Mailbox\n    config RefineryConfig\n}\n\ntype RefineryConfig struct {\n    AutoMerge     bool          // Auto-merge passing MRs\n    RunTests      bool          // Run tests before merge\n    TestCommand   string        // Command to run tests\n    RequireReview bool          // Require review before merge (future)\n}\n\nfunc NewRefinery(rig *Rig, ...) *Refinery\n\n// Lifecycle\nfunc (r *Refinery) Start() error\nfunc (r *Refinery) Stop() error\nfunc (r *Refinery) IsRunning() bool\n\n// Processing\nfunc (r *Refinery) ProcessQueue() error\nfunc (r *Refinery) ProcessMR(mr *MergeRequest) error\n```\n\n## Processing Loop\n\n1. Check queue for pending MRs\n2. For each pending MR:\n   a. Fetch polecat branch\n   b. Attempt merge to refinery/rig (local main)\n   c. Run tests if configured\n   d. If pass: push to origin, mark merged\n   e. If fail: mark rejected, notify polecat\n3. Sleep, repeat\n\n## Merge Strategy\n\n- Fast-forward when possible\n- Merge commit when not\n- On conflict: reject MR, polecat must rebase\n\n## Test Integration\n\nIf tests configured:\n```bash\ncd refinery/rig\ngit merge polecat/branch\n\u003ctest_command\u003e  # e.g., go test ./...\n```\nResult determines merge/reject.\n\n## Notifications\n\nOn merge success:\n- Mail to polecat: \"Your work merged\"\n- Update bead if issue tracked\n\nOn merge failure:\n- Mail to polecat: \"Merge failed: \u003creason\u003e\"\n- Include conflict details if applicable\n\n## Dependencies\n\nNeeds: Rig management, Git wrapper, Mail system, Merge queue","status":"closed","issue_type":"task","created_at":"2025-12-15T23:22:08.498771-08:00","updated_at":"2025-12-16T14:20:35.032221-08:00","closed_at":"2025-12-16T14:20:35.032221-08:00","dependencies":[{"issue_id":"gt-ov2","depends_on_id":"gt-u1j.14","type":"blocks","created_at":"2025-12-15T23:22:21.801826-08:00","created_by":"daemon"},{"issue_id":"gt-ov2","depends_on_id":"gt-u1j.6","type":"blocks","created_at":"2025-12-15T23:22:21.89716-08:00","created_by":"daemon"}]}
 {"id":"gt-ox9","title":"Test from Mayor","description":"This is a test message via GGT mail","status":"closed","priority":2,"issue_type":"message","created_at":"2025-12-16T22:04:31.483843-08:00","updated_at":"2025-12-16T22:06:41.127633-08:00","closed_at":"2025-12-16T22:06:41.127633-08:00"}
+{"id":"gt-p9zh","title":"gt doctor: detect orphaned code on beads-sync branch","description":"After merging beads-sync to main, some code changes can be lost if the merge conflict resolution drops files.\n\nAdd a doctor check that runs:\n  git diff main..beads-sync -- '*.go' '*.md'\n\nIf there are differences in code files (not just .beads/), warn about potentially orphaned work.\n\nToday's incident: Merge 96c773f lost mailbox.go and router.go changes from 5791752, requiring re-implementation.\n\nAcceptance:\n- gt doctor warns if beads-sync has unmerged code changes\n- Excludes .beads/ directory (expected to differ)\n- Shows file list of orphaned changes","status":"in_progress","priority":2,"issue_type":"feature","created_at":"2025-12-20T22:01:56.794648-08:00","updated_at":"2025-12-20T22:03:07.466835-08:00"}
 {"id":"gt-pc5d","title":"Recover stale polecat work: 4 branches with unpushed commits","description":"During observation of polecat workflow, found 4 polecats with unpushed work:\n\n## Branches Pushed (preserved)\n- polecat/capable: 3 commits (molecule catalog, doctor orphan detection, gt done)\n- polecat/dementus: 4 commits (Witness MVP, handoff fixes)\n- polecat/furiosa: 2 commits (bulk polecat removal, spawn handoff)\n- polecat/rictus: 1 commit (molecule docs)\n\n## Action Required\n1. Review each branch for merge-worthiness\n2. Either:\n   a. Create PRs for valuable work\n   b. OR discard if superseded\n3. After decision, clean up polecats properly\n\n## Root Cause\nPolecats were not cleaned up after previous work sessions. This is exactly why we need:\n- gt-u1k: gt shutdown should fully cleanup polecats\n- gt-8v8: Refuse to lose uncommitted work\n- gt-9nf: Always create fresh polecats","status":"open","priority":1,"issue_type":"chore","created_at":"2025-12-20T15:24:29.232772-08:00","updated_at":"2025-12-20T15:24:29.232772-08:00"}
 {"id":"gt-pio","title":"Plugin: merge-oracle (merge queue analysis)","description":"Example plugin that analyzes changesets before Refinery processes them. Builds overlap graph, classifies disjointness (parallel-safe vs needs-sequencing), uses LLM for semantic complexity, identifies high-risk patterns. Based on merge-orchestration proposal. See docs/architecture.md.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-15T22:53:04.027073-08:00","updated_at":"2025-12-15T23:17:06.507108-08:00","dependencies":[{"issue_id":"gt-pio","depends_on_id":"gt-axz","type":"blocks","created_at":"2025-12-15T22:53:17.507459-08:00","created_by":"daemon"}]}
 {"id":"gt-pnu4","title":"Test","description":"Body","status":"open","priority":2,"issue_type":"message","assignee":"gastown/alpha","created_at":"2025-12-20T21:38:39.019559-08:00","updated_at":"2025-12-20T21:38:39.019559-08:00","sender":"Steve Yegge","ephemeral":true}