fix: prevent cleanup from removing sessions with open PRs

packages/core/src/__tests__/session-manager.test.ts

@@ -1129,6 +1129,100 @@ describe("cleanup", () => {
     expect(result.skipped).toContain("app-orchestrator");
   });
 
+  it("skips dead-runtime sessions with open PRs (fixes #146)", async () => {
+    const deadRuntime: Runtime = {
+      ...mockRuntime,
+      isAlive: vi.fn().mockResolvedValue(false),
+    };
+    const openPRSCM: SCM = {
+      name: "mock-scm",
+      detectPR: vi.fn(),
+      getPRState: vi.fn().mockResolvedValue("open"),
+      mergePR: vi.fn(),
+      closePR: vi.fn(),
+      getCIChecks: vi.fn(),
+      getCISummary: vi.fn(),
+      getReviews: vi.fn(),
+      getReviewDecision: vi.fn(),
+      getPendingComments: vi.fn(),
+      getAutomatedComments: vi.fn(),
+      getMergeability: vi.fn(),
+    };
+    const registryWithDeadAndSCM: PluginRegistry = {
+      ...mockRegistry,
+      get: vi.fn().mockImplementation((slot: string) => {
+        if (slot === "runtime") return deadRuntime;
+        if (slot === "agent") return mockAgent;
+        if (slot === "workspace") return mockWorkspace;
+        if (slot === "scm") return openPRSCM;
+        return null;
+      }),
+    };
+
+    writeMetadata(sessionsDir, "app-1", {
+      worktree: "/tmp",
+      branch: "feat/create-from-scratch",
+      status: "starting",
+      project: "my-app",
+      pr: "https://github.com/org/repo/pull/99",
+      runtimeHandle: JSON.stringify(makeHandle("rt-1")),
+    });
+
+    const sm = createSessionManager({ config, registry: registryWithDeadAndSCM });
+    const result = await sm.cleanup();
+
+    // Session with open PR should NOT be killed even though runtime is dead
+    expect(result.killed).toHaveLength(0);
+    expect(result.skipped).toContain("app-1");
+  });
+
+  it("conservatively skips dead-runtime sessions when PR state check fails", async () => {
+    const deadRuntime: Runtime = {
+      ...mockRuntime,
+      isAlive: vi.fn().mockResolvedValue(false),
+    };
+    const failingSCM: SCM = {
+      name: "mock-scm",
+      detectPR: vi.fn(),
+      getPRState: vi.fn().mockRejectedValue(new Error("API error")),
+      mergePR: vi.fn(),
+      closePR: vi.fn(),
+      getCIChecks: vi.fn(),
+      getCISummary: vi.fn(),
+      getReviews: vi.fn(),
+      getReviewDecision: vi.fn(),
+      getPendingComments: vi.fn(),
+      getAutomatedComments: vi.fn(),
+      getMergeability: vi.fn(),
+    };
+    const registryWithDeadAndFailing: PluginRegistry = {
+      ...mockRegistry,
+      get: vi.fn().mockImplementation((slot: string) => {
+        if (slot === "runtime") return deadRuntime;
+        if (slot === "agent") return mockAgent;
+        if (slot === "workspace") return mockWorkspace;
+        if (slot === "scm") return failingSCM;
+        return null;
+      }),
+    };
+
+    writeMetadata(sessionsDir, "app-1", {
+      worktree: "/tmp",
+      branch: "feat/something",
+      status: "working",
+      project: "my-app",
+      pr: "https://github.com/org/repo/pull/50",
+      runtimeHandle: JSON.stringify(makeHandle("rt-1")),
+    });
+
+    const sm = createSessionManager({ config, registry: registryWithDeadAndFailing });
+    const result = await sm.cleanup();
+
+    // When PR state can't be verified, be conservative and skip
+    expect(result.killed).toHaveLength(0);
+    expect(result.skipped).toContain("app-1");
+  });
+
   it("kills sessions with dead runtimes", async () => {
     const deadRuntime: Runtime = {
       ...mockRuntime,

packages/core/src/session-manager.ts

@@ -888,11 +888,27 @@ export function createSessionManager(deps: SessionManagerDeps): SessionManager {
           }
         }
 
-        // Check if runtime is dead
+        // Check if runtime is dead — but never kill a session with an open PR.
+        // A dead runtime with an open PR means the session crashed or failed to
+        // start; the PR is orphaned and needs human attention, not silent removal.
+        // (fixes #146)
         if (!shouldKill && session.runtimeHandle && plugins.runtime) {
           try {
             const alive = await plugins.runtime.isAlive(session.runtimeHandle);
-            if (!alive) shouldKill = true;
+            if (!alive) {
+              // Guard: if session has an open PR, skip cleanup
+              let hasOpenPR = false;
+              if (session.pr && plugins.scm) {
+                try {
+                  const prState = await plugins.scm.getPRState(session.pr);
+                  if (prState === PR_STATE.OPEN) hasOpenPR = true;
+                } catch {
+                  // Can't verify PR state — be conservative, assume open
+                  hasOpenPR = true;
+                }
+              }
+              if (!hasOpenPR) shouldKill = true;
+            }
           } catch {
             // Can't check — skip
           }