[codex] Harden execution reliability and heartbeat tooling (#3679)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - Reliable execution depends on heartbeat routing, issue lifecycle
semantics, telemetry, and a fast enough local verification loop to keep
regressions visible
> - The remaining commits on this branch were mostly server/runtime
correctness fixes plus test and documentation follow-ups in that area
> - Those changes are logically separate from the UI-focused
issue-detail and workspace/navigation branches even when they touch
overlapping issue APIs
> - This pull request groups the execution reliability, heartbeat,
telemetry, and tooling changes into one standalone branch
> - The benefit is a focused review of the control-plane correctness
work, including the follow-up fix that restored the implicit
comment-reopen helpers after branch splitting

## What Changed

- Hardened issue/heartbeat execution behavior, including self-review
stage skipping, deferred mention wakes during active execution, stranded
execution recovery, active-run scoping, assignee resolution, and
blocked-to-todo wake resumption
- Reduced noisy polling/logging overhead by trimming issue run payloads,
compacting persisted run logs, silencing high-volume request logs, and
capping heartbeat-run queries in dashboard/inbox surfaces
- Expanded telemetry and status semantics with adapter/model fields on
task completion plus clearer status guidance in docs/onboarding material
- Updated test infrastructure and verification defaults with faster
route-test module isolation, cheaper default `pnpm test`, e2e isolation
from local state, and repo verification follow-ups
- Included docs/release housekeeping from the branch and added a small
follow-up commit restoring the implicit comment-reopen helpers that were
dropped during branch reconstruction

## Verification

- `pnpm vitest run
server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-telemetry-routes.test.ts`
- `pnpm vitest run server/src/__tests__/http-log-policy.test.ts
server/src/__tests__/heartbeat-run-log.test.ts
server/src/__tests__/health.test.ts`
- `server/src/__tests__/activity-service.test.ts`,
`server/src/__tests__/heartbeat-comment-wake-batching.test.ts`, and
`server/src/__tests__/heartbeat-process-recovery.test.ts` were attempted
on this host but the embedded Postgres harness reported
init-script/data-dir problems and skipped or failed to start, so they
are noted as environment-limited

## Risks

- Medium: this branch changes core issue/heartbeat routing and
reopen/wakeup behavior, so regressions would affect agent execution flow
rather than isolated UI polish
- Because it also updates verification infrastructure, reviewers should
pay attention to whether the new tests are asserting the right failure
modes and not just reshaping harness behavior

## Model Used

- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution enabled

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [ ] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

server/src/__tests__/agent-live-run-routes.test.ts

@@ -1,8 +1,6 @@
 import express from "express";
 import request from "supertest";
 import { beforeEach, describe, expect, it, vi } from "vitest";
-import { agentRoutes } from "../routes/agents.js";
-import { errorHandler } from "../middleware/index.js";
 
 const mockAgentService = vi.hoisted(() => ({
   getById: vi.fn(),
@@ -18,31 +16,37 @@ const mockIssueService = vi.hoisted(() => ({
   getByIdentifier: vi.fn(),
 }));
 
-vi.mock("../services/index.js", () => ({
-  agentService: () => mockAgentService,
-  agentInstructionsService: () => ({}),
-  accessService: () => ({}),
-  approvalService: () => ({}),
-  companySkillService: () => ({ listRuntimeSkillEntries: vi.fn() }),
-  budgetService: () => ({}),
-  heartbeatService: () => mockHeartbeatService,
-  issueApprovalService: () => ({}),
-  issueService: () => mockIssueService,
-  logActivity: vi.fn(),
-  secretService: () => ({}),
-  syncInstructionsBundleConfigFromFilePath: vi.fn((_agent, config) => config),
-  workspaceOperationService: () => ({}),
-}));
+function registerModuleMocks() {
+  vi.doMock("../services/index.js", () => ({
+    agentService: () => mockAgentService,
+    agentInstructionsService: () => ({}),
+    accessService: () => ({}),
+    approvalService: () => ({}),
+    companySkillService: () => ({ listRuntimeSkillEntries: vi.fn() }),
+    budgetService: () => ({}),
+    heartbeatService: () => mockHeartbeatService,
+    issueApprovalService: () => ({}),
+    issueService: () => mockIssueService,
+    logActivity: vi.fn(),
+    secretService: () => ({}),
+    syncInstructionsBundleConfigFromFilePath: vi.fn((_agent, config) => config),
+    workspaceOperationService: () => ({}),
+  }));
 
-vi.mock("../adapters/index.js", () => ({
-  findServerAdapter: vi.fn(),
-  listAdapterModels: vi.fn(),
-  detectAdapterModel: vi.fn(),
-  findActiveServerAdapter: vi.fn(),
-  requireServerAdapter: vi.fn(),
-}));
+  vi.doMock("../adapters/index.js", () => ({
+    findServerAdapter: vi.fn(),
+    listAdapterModels: vi.fn(),
+    detectAdapterModel: vi.fn(),
+    findActiveServerAdapter: vi.fn(),
+    requireServerAdapter: vi.fn(),
+  }));
+}
 
-function createApp() {
+async function createApp() {
+  const [{ agentRoutes }, { errorHandler }] = await Promise.all([
+    vi.importActual<typeof import("../routes/agents.js")>("../routes/agents.js"),
+    vi.importActual<typeof import("../middleware/index.js")>("../middleware/index.js"),
+  ]);
   const app = express();
   app.use(express.json());
   app.use((req, _res, next) => {
@@ -62,7 +66,14 @@ function createApp() {
 
 describe("agent live run routes", () => {
   beforeEach(() => {
-    vi.clearAllMocks();
+    vi.resetModules();
+    vi.doUnmock("../services/index.js");
+    vi.doUnmock("../adapters/index.js");
+    vi.doUnmock("../routes/agents.js");
+    vi.doUnmock("../routes/authz.js");
+    vi.doUnmock("../middleware/index.js");
+    registerModuleMocks();
+    vi.resetAllMocks();
     mockIssueService.getByIdentifier.mockResolvedValue({
       id: "issue-1",
       companyId: "company-1",
@@ -92,7 +103,7 @@ describe("agent live run routes", () => {
   });
 
   it("returns a compact active run payload for issue polling", async () => {
-    const res = await request(createApp()).get("/api/issues/PAP-1295/active-run");
+    const res = await request(await createApp()).get("/api/issues/PAP-1295/active-run");
 
     expect(res.status, JSON.stringify(res.body)).toBe(200);
     expect(mockIssueService.getByIdentifier).toHaveBeenCalledWith("PAP-1295");
@@ -114,4 +125,42 @@ describe("agent live run routes", () => {
     expect(res.body).not.toHaveProperty("contextSnapshot");
     expect(res.body).not.toHaveProperty("logRef");
   });
+
+  it("ignores a stale execution run from another issue and falls back to the assignee's matching run", async () => {
+    mockHeartbeatService.getRunIssueSummary.mockResolvedValue({
+      id: "run-foreign",
+      status: "running",
+      invocationSource: "assignment",
+      triggerDetail: "callback",
+      startedAt: new Date("2026-04-10T10:00:00.000Z"),
+      finishedAt: null,
+      createdAt: new Date("2026-04-10T09:59:00.000Z"),
+      agentId: "agent-1",
+      issueId: "issue-2",
+    });
+    mockHeartbeatService.getActiveRunIssueSummaryForAgent.mockResolvedValue({
+      id: "run-1",
+      status: "running",
+      invocationSource: "on_demand",
+      triggerDetail: "manual",
+      startedAt: new Date("2026-04-10T09:30:00.000Z"),
+      finishedAt: null,
+      createdAt: new Date("2026-04-10T09:29:59.000Z"),
+      agentId: "agent-1",
+      issueId: "issue-1",
+    });
+
+    const res = await request(await createApp()).get("/api/issues/PAP-1295/active-run");
+
+    expect(res.status, JSON.stringify(res.body)).toBe(200);
+    expect(mockHeartbeatService.getRunIssueSummary).toHaveBeenCalledWith("run-1");
+    expect(mockHeartbeatService.getActiveRunIssueSummaryForAgent).toHaveBeenCalledWith("agent-1");
+    expect(res.body).toMatchObject({
+      id: "run-1",
+      issueId: "issue-1",
+      agentId: "agent-1",
+      agentName: "Builder",
+      adapterType: "codex_local",
+    });
+  });
 });