fix(auto-start): handle survivor branch recovery in phase=complete (#2358) (#2427)

When bootstrapAutoSession finds a survivor milestone branch and the
derived state phase is "complete", recovery was skipped entirely because
the survivor branch detection only triggered for phase === "pre-planning".
This left the milestone worktree/branch alive and routed bootstrap into
showSmartEntry instead of running finalization (merge, cleanup).

Changes:
- Broaden survivor branch detection to also check phase === "complete"
- Add explicit finalization path: when hasSurvivorBranch && phase ===
  "complete", call resolver.mergeAndExit() to run the pending merge and
  worktree cleanup, then re-derive state so the normal flow continues
- After finalization, clear hasSurvivorBranch so the "all milestones
  complete" or "next milestone" path runs correctly

Fixes #2358

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/resources/extensions/gsd/auto-start.ts

@@ -297,11 +297,14 @@ export async function bootstrapAutoSession(
       }
     }
 
-    // Milestone branch recovery (#601)
+    // Milestone branch recovery (#601, #2358)
+    // Detect survivor milestone branches in both pre-planning and complete phases.
+    // In phase=complete, the milestone artifacts exist but finalization (merge,
+    // worktree cleanup) was never run — the survivor branch must be merged.
     let hasSurvivorBranch = false;
     if (
       state.activeMilestone &&
-      state.phase === "pre-planning" &&
+      (state.phase === "pre-planning" || state.phase === "complete") &&
       shouldUseWorktreeIsolation() &&
       !detectWorktreeName(base) &&
       !base.includes(`${pathSep}.gsd${pathSep}worktrees${pathSep}`)
@@ -343,6 +346,26 @@ export async function bootstrapAutoSession(
       }
     }
 
+    // Survivor branch exists and milestone is complete (#2358):
+    // The milestone artifacts were written but finalization (merge, worktree
+    // cleanup) never ran. Run mergeAndExit to finalize, then re-derive state
+    // so the normal "all milestones complete" or "next milestone" path runs.
+    if (hasSurvivorBranch && state.phase === "complete") {
+      const mid = state.activeMilestone!.id;
+      ctx.ui.notify(
+        `Milestone ${mid} is complete but branch/worktree was not finalized. Running merge now.`,
+        "info",
+      );
+      const resolver = buildResolver();
+      resolver.mergeAndExit(mid, {
+        notify: ctx.ui.notify.bind(ctx.ui),
+      });
+      invalidateAllCaches();
+      state = await deriveState(base);
+      // Clear survivor flag — finalization is done
+      hasSurvivorBranch = false;
+    }
+
     if (!hasSurvivorBranch) {
       // No active work — start a new milestone via discuss flow
       if (!state.activeMilestone || state.phase === "complete") {

src/resources/extensions/gsd/tests/survivor-branch-complete.test.ts

@@ -0,0 +1,108 @@
+/**
+ * Regression test for #2358: Survivor branch recovery skipped in phase=complete.
+ *
+ * When bootstrapAutoSession finds a survivor milestone branch and the derived
+ * state phase is "complete", recovery/finalization is skipped entirely because
+ * the survivor branch detection only triggers when phase === "pre-planning".
+ * The milestone finalization (merge, cleanup) never runs, leaving the worktree
+ * and branch alive.
+ *
+ * The fix broadens the survivor branch detection to also check phase === "complete",
+ * and adds a finalization path that runs mergeAndExit before falling through to
+ * the normal "complete" handling.
+ */
+
+import { createTestContext } from "./test-helpers.ts";
+
+const { assertTrue, assertEq, report } = createTestContext();
+
+// ═══ Test: survivor branch detection conditions ══════════════════════════════
+
+// The survivor branch detection block in auto-start.ts checks:
+//   state.activeMilestone &&
+//   state.phase === "pre-planning" &&  // <-- BUG: too restrictive
+//   shouldUseWorktreeIsolation() &&
+//   !detectWorktreeName(base) &&
+//   !base.includes(...)
+//
+// The fix should also include state.phase === "complete".
+
+{
+  console.log("\n=== #2358: survivor branch should be detected in phase=complete ===");
+
+  // Simulate the condition check before the fix (only pre-planning)
+  const phasesBeforeFix = ["pre-planning"];
+  const phasesAfterFix = ["pre-planning", "complete"];
+
+  const testPhase = "complete";
+
+  const detectedBefore = phasesBeforeFix.includes(testPhase);
+  assertEq(detectedBefore, false, "before fix: phase=complete should NOT trigger survivor detection");
+
+  const detectedAfter = phasesAfterFix.includes(testPhase);
+  assertEq(detectedAfter, true, "after fix: phase=complete SHOULD trigger survivor detection");
+}
+
+// ═══ Test: pre-planning survivor detection still works ═══════════════════════
+
+{
+  console.log("\n=== #2358: pre-planning survivor detection is not broken ===");
+
+  const phasesAfterFix = ["pre-planning", "complete"];
+  const testPhase = "pre-planning";
+
+  const detected = phasesAfterFix.includes(testPhase);
+  assertEq(detected, true, "pre-planning should still trigger survivor detection after fix");
+}
+
+// ═══ Test: other phases do NOT trigger survivor detection ════════════════════
+
+{
+  console.log("\n=== #2358: other phases should NOT trigger survivor detection ===");
+
+  const phasesAfterFix = ["pre-planning", "complete"];
+
+  for (const phase of ["planning", "executing", "blocked", "needs-discussion"]) {
+    const detected = phasesAfterFix.includes(phase);
+    assertEq(detected, false, `phase=${phase} should NOT trigger survivor detection`);
+  }
+}
+
+// ═══ Test: phase=complete + hasSurvivorBranch should trigger finalization ═════
+
+{
+  console.log("\n=== #2358: phase=complete + survivor branch triggers finalization path ===");
+
+  // Simulate the decision logic after the fix:
+  // if (hasSurvivorBranch && state.phase === "complete") -> finalize
+  // if (hasSurvivorBranch && state.phase === "needs-discussion") -> discuss
+  // if (!hasSurvivorBranch && state.phase === "complete") -> showSmartEntry
+
+  const scenarios = [
+    { hasSurvivorBranch: true, phase: "complete", expected: "finalize" },
+    { hasSurvivorBranch: true, phase: "needs-discussion", expected: "discuss" },
+    { hasSurvivorBranch: true, phase: "pre-planning", expected: "continue" },
+    { hasSurvivorBranch: false, phase: "complete", expected: "showSmartEntry" },
+  ];
+
+  for (const { hasSurvivorBranch, phase, expected } of scenarios) {
+    let result: string;
+    if (hasSurvivorBranch && phase === "complete") {
+      result = "finalize";
+    } else if (hasSurvivorBranch && phase === "needs-discussion") {
+      result = "discuss";
+    } else if (!hasSurvivorBranch && (!phase || phase === "complete")) {
+      result = "showSmartEntry";
+    } else {
+      result = "continue";
+    }
+
+    assertEq(
+      result,
+      expected,
+      `hasSurvivorBranch=${hasSurvivorBranch}, phase=${phase} -> expected ${expected}, got ${result}`,
+    );
+  }
+}
+
+report();