[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__/cli-auth-routes.test.ts

@@ -1,8 +1,6 @@
 import express from "express";
 import request from "supertest";
 import { beforeEach, describe, expect, it, vi } from "vitest";
-import { accessRoutes } from "../routes/access.js";
-import { errorHandler } from "../middleware/index.js";
 
 const mockAccessService = vi.hoisted(() => ({
   isInstanceAdmin: vi.fn(),
@@ -36,7 +34,22 @@ vi.mock("../services/index.js", () => ({
   deduplicateAgentName: vi.fn((name: string) => name),
 }));
 
-function createApp(actor: any) {
+function registerModuleMocks() {
+  vi.doMock("../services/index.js", () => ({
+    accessService: () => mockAccessService,
+    agentService: () => mockAgentService,
+    boardAuthService: () => mockBoardAuthService,
+    logActivity: mockLogActivity,
+    notifyHireApproved: vi.fn(),
+    deduplicateAgentName: vi.fn((name: string) => name),
+  }));
+}
+
+async function createApp(actor: any) {
+  const [{ accessRoutes }, { errorHandler }] = await Promise.all([
+    vi.importActual<typeof import("../routes/access.js")>("../routes/access.js"),
+    vi.importActual<typeof import("../middleware/index.js")>("../middleware/index.js"),
+  ]);
   const app = express();
   app.use(express.json());
   app.use((req, _res, next) => {
@@ -58,6 +71,10 @@ function createApp(actor: any) {
 
 describe("cli auth routes", () => {
   beforeEach(() => {
+    vi.resetModules();
+    vi.doUnmock("../routes/access.js");
+    vi.doUnmock("../middleware/index.js");
+    registerModuleMocks();
     vi.resetAllMocks();
   });
 
@@ -71,7 +88,7 @@ describe("cli auth routes", () => {
       pendingBoardToken: "pcp_board_token",
     });
 
-    const app = createApp({ type: "none", source: "none" });
+    const app = await createApp({ type: "none", source: "none" });
     const res = await request(app)
       .post("/api/cli-auth/challenges")
       .send({
@@ -107,7 +124,7 @@ describe("cli auth routes", () => {
       approvedByUser: null,
     });
 
-    const app = createApp({ type: "none", source: "none" });
+    const app = await createApp({ type: "none", source: "none" });
     const res = await request(app).get("/api/cli-auth/challenges/challenge-1?token=pcp_cli_auth_secret");
 
     expect(res.status).toBe(200);
@@ -133,7 +150,7 @@ describe("cli auth routes", () => {
     });
     mockBoardAuthService.resolveBoardActivityCompanyIds.mockResolvedValue(["company-1"]);
 
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "user-1",
       source: "session",
@@ -173,7 +190,7 @@ describe("cli auth routes", () => {
     });
     mockBoardAuthService.resolveBoardActivityCompanyIds.mockResolvedValue(["company-a", "company-b"]);
 
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "admin-1",
       source: "session",
@@ -200,7 +217,7 @@ describe("cli auth routes", () => {
     });
     mockBoardAuthService.resolveBoardActivityCompanyIds.mockResolvedValue(["company-z"]);
 
-    const app = createApp({
+    const app = await createApp({
       type: "board",
       userId: "admin-2",
       keyId: "board-key-3",