diff --git a/server/src/__tests__/issue-thread-interactions-service.test.ts b/server/src/__tests__/issue-thread-interactions-service.test.ts
index 845eb42ffba..ba8e529f6ff 100644
--- a/server/src/__tests__/issue-thread-interactions-service.test.ts
+++ b/server/src/__tests__/issue-thread-interactions-service.test.ts
@@ -1345,13 +1345,23 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
   });
 
   describe("workspace_finalize accept gate", () => {
-    async function seedAcceptGateFixture() {
+    type AcceptGateInteractionKind = "request_confirmation" | "request_checkbox_confirmation";
+
+    async function seedAcceptGateFixture(options?: {
+      kind?: AcceptGateInteractionKind;
+      sourceRunId?: string | null;
+    }) {
       const companyId = randomUUID();
       const projectId = randomUUID();
       const projectWorkspaceId = randomUUID();
       const executionWorkspaceId = randomUUID();
       const issueId = randomUUID();
       const goalId = randomUUID();
+      const agentId = randomUUID();
+      const sourceRunId =
+        options?.sourceRunId === null ? null : options?.sourceRunId ?? randomUUID();
+      const foreignRunId = randomUUID();
+      const kind = options?.kind ?? "request_confirmation";
 
       await db.insert(companies).values({
         id: companyId,
@@ -1375,6 +1385,40 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
         visibility: "default",
         isPrimary: true,
       });
+      await db.insert(agents).values({
+        id: agentId,
+        companyId,
+        name: "CodexCoder",
+        role: "engineer",
+        status: "active",
+        adapterType: "codex_local",
+        adapterConfig: {},
+        runtimeConfig: {},
+        permissions: {},
+      });
+      await db.insert(heartbeatRuns).values([
+        ...(sourceRunId
+          ? [
+              {
+                id: sourceRunId,
+                companyId,
+                agentId,
+                invocationSource: "manual",
+                status: "succeeded",
+                startedAt: new Date("2026-05-23T21:55:00.000Z"),
+                finishedAt: new Date("2026-05-23T22:05:00.000Z"),
+              },
+            ]
+          : []),
+        {
+          id: foreignRunId,
+          companyId,
+          agentId,
+          invocationSource: "manual",
+          status: "running",
+          startedAt: new Date("2026-05-23T22:10:00.000Z"),
+        },
+      ]);
       await db.insert(executionWorkspaces).values({
         id: executionWorkspaceId,
         companyId,
@@ -1404,107 +1448,63 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
         executionWorkspaceId,
       });
 
+      const payload = kind === "request_checkbox_confirmation"
+        ? {
+            version: 1 as const,
+            prompt: "Which files should be accepted?",
+            options: [
+              { id: "file-a", label: "a.txt" },
+              { id: "file-b", label: "b.txt" },
+            ],
+            minSelected: 0,
+            maxSelected: 2,
+          }
+        : {
+            version: 1 as const,
+            prompt: "Mark this issue done?",
+          };
+
       const created = await interactionsSvc.create({
         id: issueId,
         companyId,
       }, {
-        kind: "request_confirmation",
+        kind,
         continuationPolicy: "wake_assignee",
-        payload: {
-          version: 1,
-          prompt: "Mark this issue done?",
-        },
+        sourceRunId,
+        payload,
       }, {
         userId: "local-board",
       });
 
-      return { companyId, projectId, executionWorkspaceId, issueId, goalId, interactionId: created.id };
+      return {
+        companyId,
+        projectId,
+        executionWorkspaceId,
+        issueId,
+        goalId,
+        interactionId: created.id,
+        sourceRunId,
+        foreignRunId,
+      };
     }
 
-    it("refuses accept when the issue's latest workspace operation is not a successful workspace_finalize", async () => {
-      const { companyId, executionWorkspaceId, issueId, goalId, interactionId } = await seedAcceptGateFixture();
-
-      // A run touched the workspace (prepare) but never recorded workspace_finalize.
-      await db.insert(workspaceOperations).values({
-        companyId,
-        executionWorkspaceId,
-        phase: "worktree_prepare",
-        status: "succeeded",
-        startedAt: new Date("2026-05-23T22:00:00.000Z"),
-      });
-
-      await expect(
-        interactionsSvc.acceptInteraction(
-          { id: issueId, companyId, goalId, projectId: null },
-          interactionId,
-          {},
-          { userId: "local-board" },
-        ),
-      ).rejects.toMatchObject({
-        status: 409,
-        details: { executionWorkspaceId },
-      });
-
-      const row = await db
-        .select()
-        .from(issueThreadInteractions)
-        .where(eq(issueThreadInteractions.id, interactionId))
-        .then((rows) => rows[0]);
-      expect(row?.status).toBe("pending");
-    });
-
-    it("refuses accept when the latest workspace operation is a failed workspace_finalize", async () => {
-      const { companyId, executionWorkspaceId, issueId, goalId, interactionId } = await seedAcceptGateFixture();
+    it("allows request_confirmation accept when the source run finalized but a foreign run is mid-flight", async () => {
+      const { companyId, executionWorkspaceId, issueId, goalId, interactionId, sourceRunId, foreignRunId } =
+        await seedAcceptGateFixture();
 
       await db.insert(workspaceOperations).values({
         companyId,
         executionWorkspaceId,
-        phase: "worktree_prepare",
+        heartbeatRunId: sourceRunId,
+        phase: "workspace_finalize",
         status: "succeeded",
         startedAt: new Date("2026-05-23T22:00:00.000Z"),
       });
       await db.insert(workspaceOperations).values({
         companyId,
         executionWorkspaceId,
-        phase: "workspace_finalize",
-        status: "failed",
-        startedAt: new Date("2026-05-23T22:05:00.000Z"),
-      });
-
-      await expect(
-        interactionsSvc.acceptInteraction(
-          { id: issueId, companyId, goalId, projectId: null },
-          interactionId,
-          {},
-          { userId: "local-board" },
-        ),
-      ).rejects.toMatchObject({
-        status: 409,
-        details: { executionWorkspaceId },
-      });
-
-      const row = await db
-        .select()
-        .from(issueThreadInteractions)
-        .where(eq(issueThreadInteractions.id, interactionId))
-        .then((rows) => rows[0]);
-      expect(row?.status).toBe("pending");
-    });
-
-    it("allows accept once a successful workspace_finalize lands as the latest operation", async () => {
-      const { companyId, executionWorkspaceId, issueId, goalId, interactionId } = await seedAcceptGateFixture();
-
-      await db.insert(workspaceOperations).values({
-        companyId,
-        executionWorkspaceId,
-        phase: "workspace_finalize",
-        status: "failed",
-        startedAt: new Date("2026-05-23T22:05:00.000Z"),
-      });
-      await db.insert(workspaceOperations).values({
-        companyId,
-        executionWorkspaceId,
-        phase: "workspace_finalize",
+        heartbeatRunId: foreignRunId,
+        phase: "worktree_prepare",
         status: "succeeded",
         startedAt: new Date("2026-05-23T22:10:00.000Z"),
       });
@@ -1518,6 +1518,208 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
 
       expect(accepted.interaction).toMatchObject({
         id: interactionId,
+        kind: "request_confirmation",
+        status: "accepted",
+      });
+    });
+
+    it("refuses request_confirmation accept until the source run records a successful workspace_finalize", async () => {
+      const { companyId, executionWorkspaceId, issueId, goalId, interactionId, sourceRunId } =
+        await seedAcceptGateFixture();
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: sourceRunId,
+        phase: "worktree_prepare",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:00:00.000Z"),
+      });
+
+      await expect(
+        interactionsSvc.acceptInteraction(
+          { id: issueId, companyId, goalId, projectId: null },
+          interactionId,
+          {},
+          { userId: "local-board" },
+        ),
+      ).rejects.toMatchObject({
+        status: 409,
+        message: expect.stringContaining(
+          "the run that created this interaction has not finished syncing its workspace",
+        ),
+        details: { executionWorkspaceId, sourceRunId },
+      });
+
+      const row = await db
+        .select()
+        .from(issueThreadInteractions)
+        .where(eq(issueThreadInteractions.id, interactionId))
+        .then((rows) => rows[0]);
+      expect(row?.status).toBe("pending");
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: sourceRunId,
+        phase: "workspace_finalize",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:05:00.000Z"),
+      });
+
+      const accepted = await interactionsSvc.acceptInteraction(
+        { id: issueId, companyId, goalId, projectId: null },
+        interactionId,
+        {},
+        { userId: "local-board" },
+      );
+
+      expect(accepted.interaction).toMatchObject({
+        id: interactionId,
+        kind: "request_confirmation",
+        status: "accepted",
+      });
+    });
+
+    it("allows request_confirmation accept when sourceRunId is null", async () => {
+      const { companyId, executionWorkspaceId, issueId, goalId, interactionId, foreignRunId } =
+        await seedAcceptGateFixture({ sourceRunId: null });
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: foreignRunId,
+        phase: "worktree_prepare",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:10:00.000Z"),
+      });
+
+      const accepted = await interactionsSvc.acceptInteraction(
+        { id: issueId, companyId, goalId, projectId: null },
+        interactionId,
+        {},
+        { userId: "local-board" },
+      );
+
+      expect(accepted.interaction).toMatchObject({
+        id: interactionId,
+        kind: "request_confirmation",
+        status: "accepted",
+      });
+    });
+
+    it("allows request_checkbox_confirmation accept when the source run finalized but a foreign run is mid-flight", async () => {
+      const { companyId, executionWorkspaceId, issueId, goalId, interactionId, sourceRunId, foreignRunId } =
+        await seedAcceptGateFixture({ kind: "request_checkbox_confirmation" });
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: sourceRunId,
+        phase: "workspace_finalize",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:00:00.000Z"),
+      });
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: foreignRunId,
+        phase: "worktree_prepare",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:10:00.000Z"),
+      });
+
+      const accepted = await interactionsSvc.acceptInteraction(
+        { id: issueId, companyId, goalId, projectId: null },
+        interactionId,
+        { selectedOptionIds: ["file-b"] },
+        { userId: "local-board" },
+      );
+
+      expect(accepted.interaction).toMatchObject({
+        id: interactionId,
+        kind: "request_checkbox_confirmation",
+        status: "accepted",
+        result: {
+          selectedOptionIds: ["file-b"],
+        },
+      });
+    });
+
+    it("refuses request_checkbox_confirmation accept until the source run records a successful workspace_finalize", async () => {
+      const { companyId, executionWorkspaceId, issueId, goalId, interactionId, sourceRunId } =
+        await seedAcceptGateFixture({ kind: "request_checkbox_confirmation" });
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: sourceRunId,
+        phase: "worktree_prepare",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:00:00.000Z"),
+      });
+
+      await expect(
+        interactionsSvc.acceptInteraction(
+          { id: issueId, companyId, goalId, projectId: null },
+          interactionId,
+          { selectedOptionIds: ["file-a"] },
+          { userId: "local-board" },
+        ),
+      ).rejects.toMatchObject({
+        status: 409,
+        message: expect.stringContaining(
+          "the run that created this interaction has not finished syncing its workspace",
+        ),
+        details: { executionWorkspaceId, sourceRunId },
+      });
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: sourceRunId,
+        phase: "workspace_finalize",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:10:00.000Z"),
+      });
+
+      const accepted = await interactionsSvc.acceptInteraction(
+        { id: issueId, companyId, goalId, projectId: null },
+        interactionId,
+        { selectedOptionIds: ["file-a"] },
+        { userId: "local-board" },
+      );
+
+      expect(accepted.interaction).toMatchObject({
+        id: interactionId,
+        kind: "request_checkbox_confirmation",
+        status: "accepted",
+      });
+    });
+
+    it("allows request_checkbox_confirmation accept when sourceRunId is null", async () => {
+      const { companyId, executionWorkspaceId, issueId, goalId, interactionId, foreignRunId } =
+        await seedAcceptGateFixture({ kind: "request_checkbox_confirmation", sourceRunId: null });
+
+      await db.insert(workspaceOperations).values({
+        companyId,
+        executionWorkspaceId,
+        heartbeatRunId: foreignRunId,
+        phase: "worktree_prepare",
+        status: "succeeded",
+        startedAt: new Date("2026-05-23T22:10:00.000Z"),
+      });
+
+      const accepted = await interactionsSvc.acceptInteraction(
+        { id: issueId, companyId, goalId, projectId: null },
+        interactionId,
+        { selectedOptionIds: ["file-a"] },
+        { userId: "local-board" },
+      );
+
+      expect(accepted.interaction).toMatchObject({
+        id: interactionId,
+        kind: "request_checkbox_confirmation",
         status: "accepted",
       });
     });
@@ -1528,11 +1730,12 @@ describeEmbeddedPostgres("issueThreadInteractionService", () => {
       // workspace_finalize gate (PAPA-440) must not apply here. Without this
       // carve-out the board cannot triage suggested tasks on an issue whose
       // latest workspace op is still worktree_prepare.
-      const { companyId, executionWorkspaceId, issueId, goalId } = await seedAcceptGateFixture();
+      const { companyId, executionWorkspaceId, issueId, goalId, foreignRunId } = await seedAcceptGateFixture();
 
       await db.insert(workspaceOperations).values({
         companyId,
         executionWorkspaceId,
+        heartbeatRunId: foreignRunId,
         phase: "worktree_prepare",
         status: "succeeded",
         startedAt: new Date("2026-05-28T22:00:00.000Z"),
diff --git a/server/src/__tests__/issues-service.test.ts b/server/src/__tests__/issues-service.test.ts
index 68aecc8b32f..1074c6869e2 100644
--- a/server/src/__tests__/issues-service.test.ts
+++ b/server/src/__tests__/issues-service.test.ts
@@ -2924,6 +2924,102 @@ describeEmbeddedPostgres("issueService blockers and dependency wake readiness",
     await tempDb?.cleanup();
   });
 
+  async function seedSharedWorkspaceDependency() {
+    const companyId = randomUUID();
+    const assigneeAgentId = randomUUID();
+    const projectId = randomUUID();
+    const projectWorkspaceId = randomUUID();
+    const executionWorkspaceId = randomUUID();
+    const blockerId = randomUUID();
+    const dependentId = randomUUID();
+    const foreignIssueId = randomUUID();
+
+    await db.insert(companies).values({
+      id: companyId,
+      name: "Paperclip",
+      issuePrefix: `T${companyId.replace(/-/g, "").slice(0, 6).toUpperCase()}`,
+      requireBoardApprovalForNewAgents: false,
+    });
+    await db.insert(agents).values({
+      id: assigneeAgentId,
+      companyId,
+      name: "QA",
+      role: "qa",
+      status: "active",
+      adapterType: "claude_local",
+      adapterConfig: {},
+      runtimeConfig: {},
+      permissions: {},
+    });
+    await db.insert(projects).values({
+      id: projectId,
+      companyId,
+      name: "Shared workspace project",
+      status: "in_progress",
+    });
+    await db.insert(projectWorkspaces).values({
+      id: projectWorkspaceId,
+      companyId,
+      projectId,
+      name: "Shared workspace",
+      sourceType: "local_path",
+      visibility: "default",
+      isPrimary: true,
+    });
+    await db.insert(executionWorkspaces).values({
+      id: executionWorkspaceId,
+      companyId,
+      projectId,
+      projectWorkspaceId,
+      mode: "isolated_workspace",
+      strategyType: "git_worktree",
+      name: "Shared exec workspace",
+      status: "active",
+      providerType: "git_worktree",
+    });
+    await db.insert(issues).values([
+      {
+        id: blockerId,
+        companyId,
+        projectId,
+        title: "Predecessor",
+        status: "done",
+        priority: "medium",
+        executionWorkspaceId,
+      },
+      {
+        id: dependentId,
+        companyId,
+        projectId,
+        title: "Dependent",
+        status: "blocked",
+        priority: "medium",
+        assigneeAgentId,
+      },
+      {
+        id: foreignIssueId,
+        companyId,
+        projectId,
+        title: "Foreign in-flight issue",
+        status: "in_progress",
+        priority: "medium",
+        executionWorkspaceId,
+      },
+    ]);
+    await svc.update(dependentId, { blockedByIssueIds: [blockerId] });
+
+    return {
+      companyId,
+      assigneeAgentId,
+      projectId,
+      projectWorkspaceId,
+      executionWorkspaceId,
+      blockerId,
+      dependentId,
+      foreignIssueId,
+    };
+  }
+
   it("persists blocked-by relations and exposes both blockedBy and blocks summaries", async () => {
     const companyId = randomUUID();
     await db.insert(companies).values({
@@ -3081,86 +3177,82 @@ describeEmbeddedPostgres("issueService blockers and dependency wake readiness",
     ]);
   });
 
-  it("gates dependents on the workspace-finalize barrier when a done blocker's execution workspace has not synced back", async () => {
-    const companyId = randomUUID();
-    const assigneeAgentId = randomUUID();
-    const projectId = randomUUID();
-    const projectWorkspaceId = randomUUID();
-    const executionWorkspaceId = randomUUID();
+  it("treats done blockers on a shared workspace as ready while a foreign issue is in-flight", async () => {
+    const {
+      companyId,
+      executionWorkspaceId,
+      blockerId,
+      dependentId,
+      foreignIssueId,
+    } = await seedSharedWorkspaceDependency();
 
-    await db.insert(companies).values({
-      id: companyId,
-      name: "Paperclip",
-      issuePrefix: `T${companyId.replace(/-/g, "").slice(0, 6).toUpperCase()}`,
-      requireBoardApprovalForNewAgents: false,
-    });
-    await db.insert(agents).values({
-      id: assigneeAgentId,
+    await db.insert(workspaceOperations).values({
       companyId,
-      name: "QA",
-      role: "qa",
-      status: "active",
-      adapterType: "claude_local",
-      adapterConfig: {},
-      runtimeConfig: {},
-      permissions: {},
-    });
-    await db.insert(projects).values({
-      id: projectId,
-      companyId,
-      name: "Shared workspace project",
-      status: "in_progress",
-    });
-    await db.insert(projectWorkspaces).values({
-      id: projectWorkspaceId,
-      companyId,
-      projectId,
-      name: "Shared workspace",
-      sourceType: "local_path",
-      visibility: "default",
-      isPrimary: true,
-    });
-    await db.insert(executionWorkspaces).values({
-      id: executionWorkspaceId,
-      companyId,
-      projectId,
-      projectWorkspaceId,
-      mode: "isolated_workspace",
-      strategyType: "git_worktree",
-      name: "Shared exec workspace",
-      status: "active",
-      providerType: "git_worktree",
+      executionWorkspaceId,
+      issueId: foreignIssueId,
+      phase: "worktree_prepare",
+      status: "succeeded",
+      startedAt: new Date("2026-05-23T22:00:00.000Z"),
     });
 
-    const blockerId = randomUUID();
-    const dependentId = randomUUID();
-    await db.insert(issues).values([
-      {
-        id: blockerId,
-        companyId,
-        projectId,
-        title: "Predecessor",
-        status: "done",
-        priority: "medium",
-        executionWorkspaceId,
-      },
-      {
+    await expect(svc.listWakeableBlockedDependents(blockerId)).resolves.toEqual([
+      expect.objectContaining({
         id: dependentId,
-        companyId,
-        projectId,
-        title: "Dependent",
-        status: "blocked",
-        priority: "medium",
-        assigneeAgentId,
-      },
+        blockerIssueIds: [blockerId],
+      }),
     ]);
-    await svc.update(dependentId, { blockedByIssueIds: [blockerId] });
+    await expect(svc.getDependencyReadiness(dependentId)).resolves.toMatchObject({
+      isDependencyReady: true,
+      pendingFinalizeBlockerIssueIds: [],
+      unresolvedBlockerIssueIds: [],
+    });
+  });
 
-    // A run touched the workspace (prepare phase) but has not yet recorded
+  it("ignores unattributed pre-backfill workspace operations when checking blocker readiness", async () => {
+    const {
+      companyId,
+      executionWorkspaceId,
+      blockerId,
+      dependentId,
+    } = await seedSharedWorkspaceDependency();
+
+    await db.insert(workspaceOperations).values({
+      companyId,
+      executionWorkspaceId,
+      issueId: null,
+      phase: "worktree_prepare",
+      status: "succeeded",
+      startedAt: new Date("2026-05-23T22:00:00.000Z"),
+    });
+
+    await expect(svc.listWakeableBlockedDependents(blockerId)).resolves.toEqual([
+      expect.objectContaining({
+        id: dependentId,
+        blockerIssueIds: [blockerId],
+      }),
+    ]);
+    await expect(svc.getDependencyReadiness(dependentId)).resolves.toMatchObject({
+      isDependencyReady: true,
+      pendingFinalizeBlockerIssueIds: [],
+      unresolvedBlockerIssueIds: [],
+    });
+  });
+
+  it("gates dependents on the blocker's own workspace-finalize barrier until sync-back succeeds", async () => {
+    const {
+      companyId,
+      executionWorkspaceId,
+      blockerId,
+      dependentId,
+      assigneeAgentId,
+    } = await seedSharedWorkspaceDependency();
+
+    // The blocker touched its workspace but has not yet recorded
     // workspace_finalize — the dependent must NOT wake.
     await db.insert(workspaceOperations).values({
       companyId,
       executionWorkspaceId,
+      issueId: blockerId,
       phase: "worktree_prepare",
       status: "succeeded",
       startedAt: new Date("2026-05-23T22:00:00.000Z"),
@@ -3177,6 +3269,7 @@ describeEmbeddedPostgres("issueService blockers and dependency wake readiness",
     await db.insert(workspaceOperations).values({
       companyId,
       executionWorkspaceId,
+      issueId: blockerId,
       phase: "workspace_finalize",
       status: "failed",
       startedAt: new Date("2026-05-23T22:05:00.000Z"),
@@ -3188,6 +3281,7 @@ describeEmbeddedPostgres("issueService blockers and dependency wake readiness",
     await db.insert(workspaceOperations).values({
       companyId,
       executionWorkspaceId,
+      issueId: blockerId,
       phase: "workspace_finalize",
       status: "succeeded",
       startedAt: new Date("2026-05-23T22:10:00.000Z"),
diff --git a/server/src/routes/agents.ts b/server/src/routes/agents.ts
index d066bc86be0..ea16d1b37a3 100644
--- a/server/src/routes/agents.ts
+++ b/server/src/routes/agents.ts
@@ -3439,7 +3439,8 @@ export function agentRoutes(
     const agentId = req.query.agentId as string | undefined;
     const limitParam = req.query.limit as string | undefined;
     const limit = limitParam ? Math.max(1, Math.min(1000, parseInt(limitParam, 10) || 200)) : undefined;
-    const runs = await heartbeat.list(companyId, agentId, limit);
+    const summary = req.query.summary === "true" || req.query.summary === "1";
+    const runs = await heartbeat.list(companyId, agentId, limit, { summary });
     res.json(runs);
   });
 
diff --git a/server/src/routes/issues.ts b/server/src/routes/issues.ts
index 8e40055e9a4..2c2e6b32d6d 100644
--- a/server/src/routes/issues.ts
+++ b/server/src/routes/issues.ts
@@ -3906,6 +3906,7 @@ export function issueRoutes(
         entityType: "issue",
         entityId: issue.id,
         details: {
+          key: thread.documentKey,
           documentKey: thread.documentKey,
           documentId: thread.documentId,
           threadId: thread.id,
@@ -3990,6 +3991,7 @@ export function issueRoutes(
         entityType: "issue",
         entityId: issue.id,
         details: {
+          key: keyParsed.data,
           documentKey: keyParsed.data,
           threadId: comment.threadId,
           commentId: comment.id,
@@ -4043,6 +4045,7 @@ export function issueRoutes(
         entityType: "issue",
         entityId: issue.id,
         details: {
+          key: thread.documentKey,
           documentKey: thread.documentKey,
           documentId: thread.documentId,
           threadId: thread.id,
diff --git a/server/src/services/issue-thread-interactions.ts b/server/src/services/issue-thread-interactions.ts
index c75071eb909..fd81e5a80f6 100644
--- a/server/src/services/issue-thread-interactions.ts
+++ b/server/src/services/issue-thread-interactions.ts
@@ -39,7 +39,7 @@ import {
   suggestTasksResultSchema,
 } from "@paperclipai/shared";
 import { conflict, notFound, unprocessable } from "../errors.js";
-import { issueService, listUnfinalizedExecutionWorkspaceIds } from "./issues.js";
+import { issueService, runWorkspaceIsFinalized } from "./issues.js";
 
 type InteractionActor = {
   agentId?: string | null;
@@ -541,7 +541,10 @@ export function issueThreadInteractionService(db: Db) {
   async function assertIssueWorkspaceFinalizedForAccept(args: {
     db: Pick<Db, "select">;
     issue: { id: string; companyId: string };
+    sourceRunId: string | null;
   }) {
+    if (!args.sourceRunId) return;
+
     const executionWorkspaceId = await args.db
       .select({ executionWorkspaceId: issues.executionWorkspaceId })
       .from(issues)
@@ -550,17 +553,18 @@ export function issueThreadInteractionService(db: Db) {
 
     if (!executionWorkspaceId) return;
 
-    const unfinalized = await listUnfinalizedExecutionWorkspaceIds(
+    const isFinalized = await runWorkspaceIsFinalized(
       args.db,
       args.issue.companyId,
-      [executionWorkspaceId],
+      executionWorkspaceId,
+      args.sourceRunId,
     );
-    if (!unfinalized.has(executionWorkspaceId)) return;
+    if (isFinalized) return;
 
     throw conflict(
-      "Cannot accept interaction: the issue's most recent run has not completed workspace_finalize. "
+      "Cannot accept interaction: the run that created this interaction has not finished syncing its workspace. "
         + "Retry once the local worktree has finished syncing.",
-      { executionWorkspaceId },
+      { executionWorkspaceId, sourceRunId: args.sourceRunId },
     );
   }
 
@@ -870,7 +874,7 @@ export function issueThreadInteractionService(db: Db) {
           // workspace_finalize gate (PAPA-440) does not apply here.
           return issueThreadInteractionService(db).acceptSuggestedTasks(issue, interactionId, data, actor);
         case "request_confirmation": {
-          await assertIssueWorkspaceFinalizedForAccept({ db, issue });
+          await assertIssueWorkspaceFinalizedForAccept({ db, issue, sourceRunId: current.sourceRunId });
           const accepted = await acceptRequestConfirmation({
             issue,
             current,
@@ -884,7 +888,7 @@ export function issueThreadInteractionService(db: Db) {
           };
         }
         case "request_checkbox_confirmation": {
-          await assertIssueWorkspaceFinalizedForAccept({ db, issue });
+          await assertIssueWorkspaceFinalizedForAccept({ db, issue, sourceRunId: current.sourceRunId });
           const accepted = await acceptRequestConfirmation({
             issue,
             current,
diff --git a/server/src/services/issues.ts b/server/src/services/issues.ts
index 7060cec909b..3b51e6900e3 100644
--- a/server/src/services/issues.ts
+++ b/server/src/services/issues.ts
@@ -689,6 +689,94 @@ export async function listUnfinalizedExecutionWorkspaceIds(
   return unfinalized;
 }
 
+async function listPendingFinalizeBlockerIssueIds(
+  dbOrTx: Pick<Db, "select">,
+  companyId: string,
+  blockerWorkspacePairs: Array<{ blockerIssueId: string; executionWorkspaceId: string }>,
+): Promise<Set<string>> {
+  const pending = new Set<string>();
+  const blockerIssueIds = [...new Set(blockerWorkspacePairs.map((pair) => pair.blockerIssueId))];
+  const executionWorkspaceIds = [...new Set(blockerWorkspacePairs.map((pair) => pair.executionWorkspaceId))];
+  if (blockerIssueIds.length === 0 || executionWorkspaceIds.length === 0) return pending;
+
+  const rows = await dbOrTx
+    .select({
+      issueId: workspaceOperations.issueId,
+      executionWorkspaceId: workspaceOperations.executionWorkspaceId,
+      phase: workspaceOperations.phase,
+      status: workspaceOperations.status,
+      startedAt: workspaceOperations.startedAt,
+    })
+    .from(workspaceOperations)
+    .where(
+      and(
+        eq(workspaceOperations.companyId, companyId),
+        inArray(workspaceOperations.issueId, blockerIssueIds),
+        inArray(workspaceOperations.executionWorkspaceId, executionWorkspaceIds),
+      ),
+    );
+
+  const latestByBlockerWorkspace = new Map<string, { phase: string; status: string; startedAt: Date }>();
+  for (const row of rows) {
+    if (!row.issueId || !row.executionWorkspaceId) continue;
+    const key = `${row.issueId}:${row.executionWorkspaceId}`;
+    const current = latestByBlockerWorkspace.get(key);
+    if (!current || row.startedAt > current.startedAt) {
+      latestByBlockerWorkspace.set(key, {
+        phase: row.phase,
+        status: row.status,
+        startedAt: row.startedAt,
+      });
+    }
+  }
+
+  for (const pair of blockerWorkspacePairs) {
+    const latest = latestByBlockerWorkspace.get(`${pair.blockerIssueId}:${pair.executionWorkspaceId}`);
+    if (!latest) continue; // no attributed ops recorded -> nothing to finalize for this blocker
+    if (latest.phase === "workspace_finalize" && latest.status === "succeeded") continue;
+    pending.add(pair.blockerIssueId);
+  }
+
+  return pending;
+}
+
+/**
+ * Returns whether a specific run's operations on a specific execution workspace
+ * reached the workspace_finalize barrier.
+ *
+ * Runs with no operations on the workspace are considered finalized because
+ * they never touched the workspace state that accept/review gates protect.
+ */
+export async function runWorkspaceIsFinalized(
+  dbOrTx: Pick<Db, "select">,
+  companyId: string,
+  executionWorkspaceId: string,
+  runId: string,
+): Promise<boolean> {
+  const rows = await dbOrTx
+    .select({
+      phase: workspaceOperations.phase,
+      status: workspaceOperations.status,
+      startedAt: workspaceOperations.startedAt,
+    })
+    .from(workspaceOperations)
+    .where(
+      and(
+        eq(workspaceOperations.companyId, companyId),
+        eq(workspaceOperations.executionWorkspaceId, executionWorkspaceId),
+        eq(workspaceOperations.heartbeatRunId, runId),
+      ),
+    );
+
+  let latest: { phase: string; status: string; startedAt: Date } | null = null;
+  for (const row of rows) {
+    if (!latest || row.startedAt > latest.startedAt) latest = row;
+  }
+
+  if (!latest) return true;
+  return latest.phase === "workspace_finalize" && latest.status === "succeeded";
+}
+
 async function listIssueDependencyReadinessMap(
   dbOrTx: Pick<Db, "select">,
   companyId: string,
@@ -718,19 +806,22 @@ async function listIssueDependencyReadinessMap(
       ),
     );
 
-  // Collect executionWorkspaceIds of "done" blockers — these are the only ones
+  // Collect issue/workspace pairs of "done" blockers — these are the only ones
   // subject to the workspace-finalize barrier. Blockers that aren't done already
   // mark the dependent as not-ready and don't need a finalize check.
-  const doneBlockerWorkspaceIds = new Set<string>();
+  const doneBlockerWorkspacePairs: Array<{ blockerIssueId: string; executionWorkspaceId: string }> = [];
   for (const row of blockerRows) {
     if (row.blockerStatus === "done" && row.blockerExecutionWorkspaceId) {
-      doneBlockerWorkspaceIds.add(row.blockerExecutionWorkspaceId);
+      doneBlockerWorkspacePairs.push({
+        blockerIssueId: row.blockerIssueId,
+        executionWorkspaceId: row.blockerExecutionWorkspaceId,
+      });
     }
   }
-  const unfinalizedWorkspaceIds = await listUnfinalizedExecutionWorkspaceIds(
+  const pendingFinalizeBlockerIssueIds = await listPendingFinalizeBlockerIssueIds(
     dbOrTx,
     companyId,
-    [...doneBlockerWorkspaceIds],
+    doneBlockerWorkspacePairs,
   );
 
   for (const row of blockerRows) {
@@ -745,7 +836,7 @@ async function listIssueDependencyReadinessMap(
       current.isDependencyReady = false;
     } else if (
       row.blockerExecutionWorkspaceId &&
-      unfinalizedWorkspaceIds.has(row.blockerExecutionWorkspaceId)
+      pendingFinalizeBlockerIssueIds.has(row.blockerIssueId)
     ) {
       // Workspace-finalize barrier: the blocker's most recent run on its
       // execution workspace hasn't recorded a successful workspace_finalize.
diff --git a/ui/src/components/IssueChatThread.test.tsx b/ui/src/components/IssueChatThread.test.tsx
index 49a18356790..914f45645f3 100644
--- a/ui/src/components/IssueChatThread.test.tsx
+++ b/ui/src/components/IssueChatThread.test.tsx
@@ -12,6 +12,7 @@ import {
   VIRTUALIZED_THREAD_ROW_THRESHOLD,
   canStopIssueChatRun,
   findLatestCommentMessageIndex,
+  getVirtualizedMeasurementScrollAdjustment,
   resolveAssistantMessageFoldedState,
   resolveIssueChatHumanAuthor,
 } from "./IssueChatThread";
@@ -674,6 +675,51 @@ describe("IssueChatThread", () => {
     });
   });
 
+  it("cycles work modes and prevents default when iOS leaves the keydown code empty", () => {
+    const root = createRoot(container);
+
+    act(() => {
+      root.render(
+        <MemoryRouter>
+          <IssueChatThread
+            comments={[]}
+            linkedRuns={[]}
+            timelineEvents={[]}
+            liveRuns={[]}
+            issueWorkMode="standard"
+            onAdd={async () => {}}
+            enableLiveTranscriptPolling={false}
+          />
+        </MemoryRouter>,
+      );
+    });
+
+    const composer = container.querySelector('[data-testid="issue-chat-composer"]') as HTMLDivElement | null;
+    expect(composer).not.toBeNull();
+    expect(composer?.getAttribute("data-pending-work-mode")).toBe("standard");
+
+    // iOS Safari with a hardware keyboard frequently reports an empty `code` for
+    // cmd-period. Without a `key` fallback the handler returns early, never calls
+    // preventDefault, and Safari's default cancel/dismiss closes the view.
+    const evt = new KeyboardEvent("keydown", {
+      bubbles: true,
+      cancelable: true,
+      code: "",
+      key: ".",
+      metaKey: true,
+    });
+    act(() => {
+      composer?.dispatchEvent(evt);
+    });
+
+    expect(evt.defaultPrevented).toBe(true);
+    expect(composer?.getAttribute("data-pending-work-mode")).not.toBe("standard");
+
+    act(() => {
+      root.unmount();
+    });
+  });
+
   it("virtualizes long merged threads so only a windowed slice mounts", () => {
     const root = createRoot(container);
     const totalMergedRows =
@@ -1343,6 +1389,31 @@ describe("IssueChatThread", () => {
     });
   });
 
+  it("keeps the viewport anchored when virtualized rows above it remeasure", () => {
+    expect(getVirtualizedMeasurementScrollAdjustment({
+      itemStart: 200,
+      previousSize: 220,
+      nextSize: 360,
+      viewportStart: 480,
+    })).toBe(140);
+
+    expect(getVirtualizedMeasurementScrollAdjustment({
+      itemStart: 200,
+      previousSize: 360,
+      nextSize: 180,
+      viewportStart: 620,
+    })).toBe(-180);
+  });
+
+  it("does not scroll-anchor virtualized measurement changes inside the viewport", () => {
+    expect(getVirtualizedMeasurementScrollAdjustment({
+      itemStart: 420,
+      previousSize: 220,
+      nextSize: 360,
+      viewportStart: 480,
+    })).toBe(0);
+  });
+
   it("renders virtualized rows with the same role/kind metadata as the direct path", () => {
     const root = createRoot(container);
 
diff --git a/ui/src/components/IssueChatThread.tsx b/ui/src/components/IssueChatThread.tsx
index 48b4d92244d..ccccf325a28 100644
--- a/ui/src/components/IssueChatThread.tsx
+++ b/ui/src/components/IssueChatThread.tsx
@@ -51,6 +51,7 @@ import { copyTextToClipboard } from "../lib/clipboard";
 import {
   buildIssueChatMessages,
   formatDurationWords,
+  isCoTSegmentActive,
   stabilizeThreadMessages,
   type IssueChatComment,
   type IssueChatLinkedRun,
@@ -870,13 +871,16 @@ function IssueChatChainOfThought({
     (p): p is ToolCallMessagePart => p.type === "tool-call",
   );
 
-  const isActive = isMessageRunning;
-  const [expanded, setExpanded] = useState(isActive);
-
   const rawSegments = Array.isArray(custom.chainOfThoughtSegments)
     ? (custom.chainOfThoughtSegments as SegmentTiming[])
     : [];
   const segmentTiming = myIndex >= 0 ? rawSegments[myIndex] ?? null : null;
+  const isActive = isCoTSegmentActive({
+    isMessageRunning,
+    segmentIndex: myIndex,
+    segmentCount: rawSegments.length,
+  });
+  const [expanded, setExpanded] = useState(isActive);
   const liveElapsed = useLiveElapsed(segmentTiming?.startMs, isActive);
 
   useEffect(() => {
@@ -2941,6 +2945,18 @@ type SimpleVirtualItem = {
   size: number;
 };
 
+export function getVirtualizedMeasurementScrollAdjustment(args: {
+  itemStart: number;
+  previousSize: number;
+  nextSize: number;
+  viewportStart: number;
+}) {
+  const { itemStart, previousSize, nextSize, viewportStart } = args;
+  const previousEnd = itemStart + previousSize;
+  if (previousEnd > viewportStart) return 0;
+  return nextSize - previousSize;
+}
+
 function useIssueThreadVirtualizer({
   count,
   estimateSize,
@@ -3055,7 +3071,20 @@ function useIssueThreadVirtualizer({
       const key = getItemKey(index);
       const previousSize = measuredSizeByKeyRef.current.get(key) ?? estimatedSize;
       if (Math.abs(previousSize - measuredSize) < 1) return;
+      const scrollAdjustment = getVirtualizedMeasurementScrollAdjustment({
+        itemStart: itemStarts[index] ?? scrollMargin,
+        previousSize,
+        nextSize: measuredSize,
+        viewportStart: Math.max(scrollMargin, scrollOffset()),
+      });
       measuredSizeByKeyRef.current.set(key, measuredSize);
+      if (Math.abs(scrollAdjustment) >= 1) {
+        if (mode.kind === "window") {
+          window.scrollBy({ top: scrollAdjustment, behavior: "auto" });
+        } else {
+          mode.element.scrollBy({ top: scrollAdjustment, behavior: "auto" });
+        }
+      }
       rerender((value) => value + 1);
     },
   };
@@ -3746,7 +3775,13 @@ const IssueChatComposer = forwardRef<IssueChatComposerHandle, IssueChatComposerP
   const PendingWorkModeIcon = pendingWorkModeMeta.icon;
 
   function handleComposerKeyDown(evt: ReactKeyboardEvent<HTMLDivElement>) {
-    if (!(evt.metaKey || evt.ctrlKey) || evt.code !== "Period") return;
+    // Match the period via both `code` and `key`: iOS Safari with a hardware
+    // keyboard often leaves `code` empty for cmd-period, so relying on it alone
+    // lets the event fall through and triggers Safari's default cancel/dismiss
+    // (which closes the view). Catching `key === "."` keeps the shortcut working
+    // on iOS while preserving desktop behavior.
+    const isPeriod = evt.code === "Period" || evt.key === ".";
+    if (!(evt.metaKey || evt.ctrlKey) || !isPeriod) return;
     evt.preventDefault();
     setPendingWorkMode((current) => nextWorkMode(current, true));
   }
diff --git a/ui/src/components/IssueChatThreadClassic.tsx b/ui/src/components/IssueChatThreadClassic.tsx
index 0da6f11cf35..f7188e259ce 100644
--- a/ui/src/components/IssueChatThreadClassic.tsx
+++ b/ui/src/components/IssueChatThreadClassic.tsx
@@ -61,6 +61,7 @@ import { copyTextToClipboard } from "../lib/clipboard";
 import {
   buildIssueChatMessages,
   formatDurationWords,
+  isCoTSegmentActive,
   stabilizeThreadMessages,
   type IssueChatComment,
   type IssueChatLinkedRun,
@@ -849,13 +850,16 @@ function IssueChatChainOfThought({
     (p): p is ToolCallMessagePart => p.type === "tool-call",
   );
 
-  const isActive = isMessageRunning;
-  const [expanded, setExpanded] = useState(isActive);
-
   const rawSegments = Array.isArray(custom.chainOfThoughtSegments)
     ? (custom.chainOfThoughtSegments as SegmentTiming[])
     : [];
   const segmentTiming = myIndex >= 0 ? rawSegments[myIndex] ?? null : null;
+  const isActive = isCoTSegmentActive({
+    isMessageRunning,
+    segmentIndex: myIndex,
+    segmentCount: rawSegments.length,
+  });
+  const [expanded, setExpanded] = useState(isActive);
   const liveElapsed = useLiveElapsed(segmentTiming?.startMs, isActive);
 
   useEffect(() => {
@@ -3587,7 +3591,13 @@ const IssueChatComposer = forwardRef<IssueChatComposerHandle, IssueChatComposerP
   const PendingWorkModeIcon = pendingWorkModeMeta.icon;
 
   function handleComposerKeyDown(evt: ReactKeyboardEvent<HTMLDivElement>) {
-    if (!(evt.metaKey || evt.ctrlKey) || evt.code !== "Period") return;
+    // Match the period via both `code` and `key`: iOS Safari with a hardware
+    // keyboard often leaves `code` empty for cmd-period, so relying on it alone
+    // lets the event fall through and triggers Safari's default cancel/dismiss
+    // (which closes the view). Catching `key === "."` keeps the shortcut working
+    // on iOS while preserving desktop behavior.
+    const isPeriod = evt.code === "Period" || evt.key === ".";
+    if (!(evt.metaKey || evt.ctrlKey) || !isPeriod) return;
     evt.preventDefault();
     setPendingWorkMode((current) => nextWorkMode(current, false));
   }
diff --git a/ui/src/context/LiveUpdatesProvider.test.ts b/ui/src/context/LiveUpdatesProvider.test.ts
index 673b7032b3e..f696b0b93d5 100644
--- a/ui/src/context/LiveUpdatesProvider.test.ts
+++ b/ui/src/context/LiveUpdatesProvider.test.ts
@@ -139,6 +139,9 @@ describe("LiveUpdatesProvider issue invalidation", () => {
     expect(invalidations).toContainEqual({
       queryKey: queryKeys.issues.documentRevisions("issue-1", "plan"),
     });
+    expect(invalidations).toContainEqual({
+      queryKey: ["issues", "document-annotations", "issue-1", "plan"],
+    });
     expect(invalidations).toContainEqual({
       queryKey: queryKeys.issues.documents("PAP-9403"),
     });
@@ -148,6 +151,9 @@ describe("LiveUpdatesProvider issue invalidation", () => {
     expect(invalidations).toContainEqual({
       queryKey: queryKeys.issues.documentRevisions("PAP-9403", "plan"),
     });
+    expect(invalidations).toContainEqual({
+      queryKey: ["issues", "document-annotations", "PAP-9403", "plan"],
+    });
     expect(invalidations).not.toContainEqual({
       queryKey: queryKeys.issues.documents("issue-1"),
       refetchType: "inactive",
@@ -186,6 +192,83 @@ describe("LiveUpdatesProvider issue invalidation", () => {
     expect(invalidations).toContainEqual({
       queryKey: ["issues", "document-revisions", "issue-1"],
     });
+    expect(invalidations).toContainEqual({
+      queryKey: ["issues", "document-annotations", "issue-1"],
+    });
+  });
+
+  it("refreshes document annotation caches when annotation activity arrives", () => {
+    const invalidations: unknown[] = [];
+    const queryClient = {
+      invalidateQueries: (input: unknown) => {
+        invalidations.push(input);
+      },
+      getQueryData: () => undefined,
+    };
+
+    __liveUpdatesTestUtils.invalidateActivityQueries(
+      queryClient as never,
+      "company-1",
+      {
+        entityType: "issue",
+        entityId: "issue-1",
+        action: "issue.document_annotation_comment_added",
+        actorType: "user",
+        actorId: "user-2",
+        details: {
+          identifier: "PAP-9403",
+          documentKey: "plan",
+          threadId: "thread-1",
+          commentId: "comment-1",
+        },
+      },
+      { userId: "user-1", agentId: null },
+    );
+
+    expect(invalidations).toContainEqual({
+      queryKey: ["issues", "document-annotations", "issue-1", "plan"],
+    });
+    expect(invalidations).toContainEqual({
+      queryKey: ["issues", "document-annotations", "PAP-9403", "plan"],
+    });
+    expect(invalidations).not.toContainEqual({
+      queryKey: queryKeys.issues.documents("issue-1"),
+    });
+  });
+
+  it("refreshes routine description annotation caches when routine annotation activity arrives", () => {
+    const invalidations: unknown[] = [];
+    const queryClient = {
+      invalidateQueries: (input: unknown) => {
+        invalidations.push(input);
+      },
+      getQueryData: () => undefined,
+    };
+
+    __liveUpdatesTestUtils.invalidateActivityQueries(
+      queryClient as never,
+      "company-1",
+      {
+        entityType: "routine",
+        entityId: "routine-1",
+        action: "routine.document_annotation_comment_added",
+        actorType: "user",
+        actorId: "user-2",
+        details: {
+          documentKey: "description",
+          threadId: "thread-1",
+          commentId: "comment-1",
+        },
+      },
+      { userId: "user-1", agentId: null },
+    );
+
+    expect(invalidations).toContainEqual({
+      queryKey: ["routines"],
+    });
+    expect(invalidations).toContainEqual({
+      queryKey: ["routines", "document-annotations", "routine-1", "description"],
+    });
   });
 
   it("keeps self-authored comment events from refetching the active issue tree", () => {
diff --git a/ui/src/context/LiveUpdatesProvider.tsx b/ui/src/context/LiveUpdatesProvider.tsx
index 67b5b3503a1..1e1b908360b 100644
--- a/ui/src/context/LiveUpdatesProvider.tsx
+++ b/ui/src/context/LiveUpdatesProvider.tsx
@@ -415,6 +415,20 @@ const ISSUE_DOCUMENT_ACTIVITY_ACTIONS = new Set([
   "issue.document_restored",
   "issue.document_deleted",
 ]);
+const ISSUE_DOCUMENT_ANNOTATION_ACTIVITY_ACTIONS = new Set([
+  "issue.document_annotation_thread_created",
+  "issue.document_annotation_comment_added",
+  "issue.document_annotation_thread_resolved",
+  "issue.document_annotation_thread_reopened",
+  "issue.document_annotation_remapped",
+]);
+const ROUTINE_DOCUMENT_ANNOTATION_ACTIVITY_ACTIONS = new Set([
+  "routine.document_annotation_thread_created",
+  "routine.document_annotation_comment_added",
+  "routine.document_annotation_thread_resolved",
+  "routine.document_annotation_thread_reopened",
+  "routine.document_annotation_remapped",
+]);
 const AGENT_TOAST_STATUSES = new Set(["error"]);
 const RUN_TOAST_STATUSES = new Set(["failed", "timed_out", "cancelled"]);
 
@@ -710,6 +724,18 @@ function invalidateActivityQueries(
             queryClient.invalidateQueries({ queryKey: ["issues", "document-revisions", ref], ...invalidationOptions });
           }
         }
+        if (
+          action &&
+          (ISSUE_DOCUMENT_ACTIVITY_ACTIONS.has(action) || ISSUE_DOCUMENT_ANNOTATION_ACTIVITY_ACTIONS.has(action))
+        ) {
+          const documentKey = readString(details?.key) ?? readString(details?.documentKey);
+          queryClient.invalidateQueries({
+            queryKey: documentKey
+              ? ["issues", "document-annotations", ref, documentKey]
+              : ["issues", "document-annotations", ref],
+            ...invalidationOptions,
+          });
+        }
         if (action?.startsWith("issue.thread_interaction_")) {
           queryClient.invalidateQueries({ queryKey: queryKeys.issues.interactions(ref), ...invalidationOptions });
         }
@@ -761,6 +787,12 @@ function invalidateActivityQueries(
 
   if (entityType === "routine" || entityType === "routine_trigger" || entityType === "routine_run") {
     queryClient.invalidateQueries({ queryKey: ["routines"] });
+    if (entityType === "routine" && action && ROUTINE_DOCUMENT_ANNOTATION_ACTIVITY_ACTIONS.has(action) && entityId) {
+      const documentKey = readString(details?.key) ?? readString(details?.documentKey) ?? "description";
+      queryClient.invalidateQueries({
+        queryKey: ["routines", "document-annotations", entityId, documentKey],
+      });
+    }
     return;
   }
 
diff --git a/ui/src/lib/issue-chat-messages.test.ts b/ui/src/lib/issue-chat-messages.test.ts
index 786e1b3ab20..8d1147edacd 100644
--- a/ui/src/lib/issue-chat-messages.test.ts
+++ b/ui/src/lib/issue-chat-messages.test.ts
@@ -3,6 +3,7 @@ import type { Agent } from "@paperclipai/shared";
 import {
   buildAssistantPartsFromTranscript,
   buildIssueChatMessages,
+  isCoTSegmentActive,
   stabilizeThreadMessages,
   type IssueChatComment,
   type IssueChatLinkedRun,
@@ -238,6 +239,24 @@ describe("buildAssistantPartsFromTranscript", () => {
     }]);
   });
 
+  it("marks only the latest chain-of-thought segment active while a run is live", () => {
+    expect(isCoTSegmentActive({
+      isMessageRunning: true,
+      segmentIndex: 0,
+      segmentCount: 2,
+    })).toBe(false);
+    expect(isCoTSegmentActive({
+      isMessageRunning: true,
+      segmentIndex: 1,
+      segmentCount: 2,
+    })).toBe(true);
+    expect(isCoTSegmentActive({
+      isMessageRunning: false,
+      segmentIndex: 1,
+      segmentCount: 2,
+    })).toBe(false);
+  });
+
   it("keeps run errors while suppressing init and system transcript noise", () => {
     const result = buildAssistantPartsFromTranscript([
       {
diff --git a/ui/src/lib/issue-chat-messages.ts b/ui/src/lib/issue-chat-messages.ts
index fe2d0c37c04..4993cd709ed 100644
--- a/ui/src/lib/issue-chat-messages.ts
+++ b/ui/src/lib/issue-chat-messages.ts
@@ -538,6 +538,17 @@ export interface SegmentTiming {
   endMs: number;
 }
 
+export function isCoTSegmentActive(args: {
+  isMessageRunning: boolean;
+  segmentIndex: number;
+  segmentCount: number;
+}) {
+  const { isMessageRunning, segmentIndex, segmentCount } = args;
+  if (!isMessageRunning) return false;
+  if (segmentCount <= 0 || segmentIndex < 0) return true;
+  return segmentIndex === segmentCount - 1;
+}
+
 function computeSegmentTimings(entries: readonly IssueChatTranscriptEntry[]): SegmentTiming[] {
   const timings: SegmentTiming[] = [];
   let inSegment = false;