fix(kanban): skip gone branches in merge-all instead of halting

merge-all halted with "merge: <branch> - not something we can merge" when a
candidate's branch ref no longer resolved (worktree+branch cleaned up
out-of-band while the run row lingered with branch set). That's not a
conflict — there's nothing for a resolution agent to do — yet it stopped
the whole batch.

- Verify each candidate resolves to a commit (resolveRef) before attempting;
  non-resolving branches are skipped (⤳) and the batch continues.
- Null the stale branch on the run row so it stops reappearing as a candidate.
- BatchMergeItem gains `skipped`; the modal shows skipped branches and counts
  them in the summary.
EOF && echo "" && git push 2>&1 | tail -4

apps/api/src/orchestrator/runs.ts

@@ -15,7 +15,7 @@ import { newToken, REPO_ROOT } from './config.js';
 import { buildPrompt, buildConflictResolutionPrompt } from './prompt.js';
 import { Runner, type PersistedEvent } from './runner.js';
 import { BevyProcess } from './bevy.js';
-import { attemptMerge, abortMerge, createRecoveryBranch, createWorktree, currentBranch, dirtySummary, hasMergeInProgress, headSha, isMergedIntoHead, isWorktreePresent, mainDirtySummary, removeWorktree, type BatchMergeItem, type BatchMergeResult, type Worktree } from './worktrees.js';
+import { attemptMerge, abortMerge, createRecoveryBranch, createWorktree, currentBranch, dirtySummary, hasMergeInProgress, headSha, isMergedIntoHead, isWorktreePresent, mainDirtySummary, removeWorktree, resolveRef, type BatchMergeItem, type BatchMergeResult, type Worktree } from './worktrees.js';
 
 export interface StartRunInput {
   cardId: string;
@@ -302,13 +302,25 @@ class RunManager {
 
     const seenBranch = new Set<string>();
     const candidates: { branch: string; runId: string; cardId: string }[] = [];
+    const stale: { branch: string; runId: string }[] = [];
     for (const row of rows) {
       const branch = row.branch!;
       if (seenBranch.has(branch)) continue; // dedup (e.g. multiple runs same branch)
       seenBranch.add(branch);
+      // A branch that no longer resolves to a commit means the worktree+branch
+      // were cleaned up out-of-band but the row lingered. Skip it (don't halt),
+      // and null the stale branch so it stops reappearing as a candidate.
+      if (!resolveRef(branch)) {
+        stale.push({ branch, runId: row.id });
+        continue;
+      }
       if (isMergedIntoHead(branch)) continue; // nothing to merge
       candidates.push({ branch, runId: row.id, cardId: row.card_id });
     }
+    if (stale.length > 0) {
+      const setNull = stale.map((s) => '?').join(',');
+      db.prepare(`UPDATE agent_runs SET branch = NULL WHERE id IN (${setNull})`).run(...stale.map((s) => s.runId));
+    }
 
     // Snapshot HEAD so the operator can reset the entire batch if a resolution
     // misfires (`git reset --hard <recoveryRef>`).
@@ -316,7 +328,17 @@ class RunManager {
     createRecoveryBranch(recoveryRef);
 
     this.mergeBatchInProgress = true;
-    const items: BatchMergeItem[] = [];
+    const items: BatchMergeItem[] = stale.map(({ branch, runId }) => ({
+      ok: false,
+      alreadyMerged: false,
+      conflict: false,
+      skipped: true,
+      target,
+      branch,
+      output: 'branch no longer resolves (worktree cleaned up) — skipped',
+      runId,
+      resolutionRunId: null,
+    }));
     let haltedOn: string | null = null;
     let reason: string | null = null;
 
@@ -325,14 +347,14 @@ class RunManager {
         const attempt = attemptMerge(branch);
         if (attempt.ok) {
           // Clean merge (or already-merged no-op) — nothing more to do.
-          items.push({ ok: true, alreadyMerged: attempt.alreadyMerged, conflict: false, target, branch, output: attempt.output, runId, resolutionRunId: null });
+          items.push({ ok: true, alreadyMerged: attempt.alreadyMerged, conflict: false, skipped: false, target, branch, output: attempt.output, runId, resolutionRunId: null });
           continue;
         }
         if (!attempt.conflict) {
           // Non-conflict failure (e.g. dirty mid-batch): halt, tree already clean.
           haltedOn = branch;
           reason = attempt.output;
-          items.push({ ok: false, alreadyMerged: false, conflict: false, target, branch, output: attempt.output, runId, resolutionRunId: null });
+          items.push({ ok: false, alreadyMerged: false, conflict: false, skipped: false, target, branch, output: attempt.output, runId, resolutionRunId: null });
           break;
         }
 
@@ -349,6 +371,7 @@ class RunManager {
             ok: true,
             alreadyMerged: false,
             conflict: true,
+            skipped: false,
             target,
             branch,
             output: `Conflict resolved by agent${summary ? `: ${summary}` : '.'}`,
@@ -360,7 +383,7 @@ class RunManager {
         abortMerge();
         haltedOn = branch;
         reason = `Conflict resolution agent did not complete the merge (status: ${status}). Aborted; ${target} left clean.`;
-        items.push({ ok: false, alreadyMerged: false, conflict: true, target, branch, output: reason, runId, resolutionRunId: resRunId });
+        items.push({ ok: false, alreadyMerged: false, conflict: true, skipped: false, target, branch, output: reason, runId, resolutionRunId: resRunId });
         break;
       }
     } finally {

apps/api/src/orchestrator/worktrees.ts

@@ -185,6 +185,10 @@ export interface BatchMergeItem extends MergeResult {
   conflict: boolean;
   /** When an agent resolved a conflict for this branch, its run id; else null. */
   resolutionRunId: string | null;
+  /** True if the branch couldn't be merged because it no longer resolves to a
+   * commit (worktree/branch cleaned up but the run row lingered). Such branches
+   * are skipped — the batch continues — rather than halting the whole run. */
+  skipped: boolean;
 }
 
 /** Result of merging several branches sequentially into the main branch. */
@@ -224,6 +228,19 @@ export function unmergedPaths(): string[] {
   }
 }
 
+/**
+ * Resolve a ref to its commit SHA, or null if it doesn't resolve (branch deleted,
+ * never created, dangling). Used to skip stale run records whose worktree+branch
+ * were cleaned up out-of-band but whose row still carries a `branch` value.
+ */
+export function resolveRef(ref: string): string | null {
+  try {
+    return git(['rev-parse', '--verify', '--quiet', `${ref}^{commit}`]);
+  } catch {
+    return null;
+  }
+}
+
 /** Abort an in-progress merge in the main worktree (best-effort). */
 export function abortMerge(): void {
   try {

apps/docs/src/components/kanban/MergeAllModal.tsx

@@ -56,6 +56,8 @@ export function MergeAllModal({ result, busy, onClose }: MergeAllModalProps) {
                 ` · ${result.items.filter((i) => i.conflict && i.ok).length} conflicts resolved by agent`}
               {result.items.some((i) => i.alreadyMerged) &&
                 ` · ${result.items.filter((i) => i.alreadyMerged).length} already in`}
+              {result.items.some((i) => i.skipped) &&
+                ` · ${result.items.filter((i) => i.skipped).length} skipped`}
               {result.haltedOn && ' · halted on conflict'}
             </p>
 
@@ -94,16 +96,31 @@ export function MergeAllModal({ result, busy, onClose }: MergeAllModalProps) {
             {result.items.length > 0 && (
               <div className="flex flex-col gap-2">
                 {result.items.map((item) => {
-                  const tone =
-                    item.alreadyMerged ? 'var(--muted)' : item.ok ? 'var(--green)' : 'var(--red)';
-                  const label = item.alreadyMerged
-                    ? 'already in target'
-                    : item.conflict && item.ok
-                      ? 'conflict resolved by agent'
+                  const tone = item.skipped
+                    ? 'var(--muted)'
+                    : item.alreadyMerged
+                      ? 'var(--muted)'
                       : item.ok
-                        ? 'merged'
-                        : 'conflict';
-                  const glyph = item.alreadyMerged ? '⇢' : item.conflict && item.ok ? '🤖' : item.ok ? '✓' : '⚠';
+                        ? 'var(--green)'
+                        : 'var(--red)';
+                  const label = item.skipped
+                    ? 'skipped (branch gone)'
+                    : item.alreadyMerged
+                      ? 'already in target'
+                      : item.conflict && item.ok
+                        ? 'conflict resolved by agent'
+                        : item.ok
+                          ? 'merged'
+                          : 'conflict';
+                  const glyph = item.skipped
+                    ? '⤳'
+                    : item.alreadyMerged
+                      ? '⇢'
+                      : item.conflict && item.ok
+                        ? '🤖'
+                        : item.ok
+                          ? '✓'
+                          : '⚠';
                   return (
                     <div
                       key={item.runId}

apps/docs/src/lib/orchestratorApi.ts

@@ -121,6 +121,9 @@ export interface BatchMergeItem extends MergeResult {
   conflict: boolean;
   /** When an agent resolved a conflict for this branch, its run id; else null. */
   resolutionRunId: string | null;
+  /** True if the branch no longer resolves (cleaned up but the row lingered) —
+   * skipped, batch continues. */
+  skipped: boolean;
 }
 
 /** Result of merging several branches sequentially into the main branch. */