[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__/issue-update-comment-wakeup-routes.test.ts

@@ -1,8 +1,6 @@
 import express from "express";
 import request from "supertest";
 import { beforeEach, describe, expect, it, vi } from "vitest";
-import { errorHandler } from "../middleware/index.js";
-import { issueRoutes } from "../routes/issues.js";
 
 const ASSIGNEE_AGENT_ID = "11111111-1111-4111-8111-111111111111";
 
@@ -31,6 +29,10 @@ vi.mock("../services/index.js", () => ({
   }),
   agentService: () => ({
     getById: vi.fn(async () => null),
+    resolveByReference: vi.fn(async (_companyId: string, raw: string) => ({
+      ambiguous: false,
+      agent: { id: raw },
+    })),
   }),
   documentService: () => ({}),
   executionWorkspaceService: () => ({}),
@@ -60,7 +62,53 @@ vi.mock("../services/index.js", () => ({
   workProductService: () => ({}),
 }));
 
-function createApp() {
+function registerModuleMocks() {
+  vi.doMock("../services/index.js", () => ({
+    accessService: () => ({
+      canUser: vi.fn(async () => true),
+      hasPermission: vi.fn(async () => true),
+    }),
+    agentService: () => ({
+      getById: vi.fn(async () => null),
+      resolveByReference: vi.fn(async (_companyId: string, raw: string) => ({
+        ambiguous: false,
+        agent: { id: raw },
+      })),
+    }),
+    documentService: () => ({}),
+    executionWorkspaceService: () => ({}),
+    feedbackService: () => ({
+      listIssueVotesForUser: vi.fn(async () => []),
+      saveIssueVote: vi.fn(async () => ({ vote: null, consentEnabledNow: false, sharingEnabled: false })),
+    }),
+    goalService: () => ({}),
+    heartbeatService: () => mockHeartbeatService,
+    instanceSettingsService: () => ({
+      get: vi.fn(async () => ({
+        id: "instance-settings-1",
+        general: {
+          censorUsernameInLogs: false,
+          feedbackDataSharingPreference: "prompt",
+        },
+      })),
+      listCompanyIds: vi.fn(async () => ["company-1"]),
+    }),
+    issueApprovalService: () => ({}),
+    issueService: () => mockIssueService,
+    logActivity: vi.fn(async () => undefined),
+    projectService: () => ({}),
+    routineService: () => ({
+      syncRunStatusForIssue: vi.fn(async () => undefined),
+    }),
+    workProductService: () => ({}),
+  }));
+}
+
+async function createApp() {
+  const [{ errorHandler }, { issueRoutes }] = await Promise.all([
+    vi.importActual<typeof import("../middleware/index.js")>("../middleware/index.js"),
+    vi.importActual<typeof import("../routes/issues.js")>("../routes/issues.js"),
+  ]);
   const app = express();
   app.use(express.json());
   app.use((req, _res, next) => {
@@ -101,7 +149,12 @@ function makeIssue(overrides: Record<string, unknown> = {}) {
 
 describe("issue update comment wakeups", () => {
   beforeEach(() => {
-    vi.clearAllMocks();
+    vi.resetModules();
+    vi.doUnmock("../routes/issues.js");
+    vi.doUnmock("../routes/authz.js");
+    vi.doUnmock("../middleware/index.js");
+    registerModuleMocks();
+    vi.resetAllMocks();
     mockIssueService.findMentionedAgents.mockResolvedValue([]);
     mockIssueService.getRelationSummaries.mockResolvedValue({ blockedBy: [], blocks: [] });
     mockIssueService.listWakeableBlockedDependents.mockResolvedValue([]);
@@ -123,7 +176,7 @@ describe("issue update comment wakeups", () => {
       body: "write the whole thing",
     });
 
-    const res = await request(createApp())
+    const res = await request(await createApp())
       .patch(`/api/issues/${existing.id}`)
       .send({
         assigneeAgentId: ASSIGNEE_AGENT_ID,
@@ -170,7 +223,7 @@ describe("issue update comment wakeups", () => {
       body: "please revise this",
     });
 
-    const res = await request(createApp())
+    const res = await request(await createApp())
       .patch(`/api/issues/${existing.id}`)
       .send({
         comment: "please revise this",