[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-adapter-validation-routes.test.ts

@@ -1,10 +1,7 @@
 import express from "express";
 import request from "supertest";
 import { beforeEach, afterEach, describe, expect, it, vi } from "vitest";
-import { agentRoutes } from "../routes/agents.js";
-import { errorHandler } from "../middleware/index.js";
 import type { ServerAdapterModule } from "../adapters/index.js";
-import { registerServerAdapter, unregisterServerAdapter } from "../adapters/index.js";
 
 const mockAgentService = vi.hoisted(() => ({
   create: vi.fn(),
@@ -82,6 +79,28 @@ vi.mock("../services/instance-settings.js", () => ({
   instanceSettingsService: () => mockInstanceSettingsService,
 }));
 
+function registerModuleMocks() {
+  vi.doMock("../services/index.js", () => ({
+    agentService: () => mockAgentService,
+    agentInstructionsService: () => mockAgentInstructionsService,
+    accessService: () => mockAccessService,
+    approvalService: () => mockApprovalService,
+    companySkillService: () => mockCompanySkillService,
+    budgetService: () => mockBudgetService,
+    heartbeatService: () => mockHeartbeatService,
+    issueApprovalService: () => mockIssueApprovalService,
+    issueService: () => ({}),
+    logActivity: mockLogActivity,
+    secretService: () => mockSecretService,
+    syncInstructionsBundleConfigFromFilePath: vi.fn((_agent, config) => config),
+    workspaceOperationService: () => ({}),
+  }));
+
+  vi.doMock("../services/instance-settings.js", () => ({
+    instanceSettingsService: () => mockInstanceSettingsService,
+  }));
+}
+
 const externalAdapter: ServerAdapterModule = {
   type: "external_test",
   execute: async () => ({ exitCode: 0, signal: null, timedOut: false }),
@@ -93,7 +112,13 @@ const externalAdapter: ServerAdapterModule = {
   }),
 };
 
-function createApp() {
+const missingAdapterType = "missing_adapter_validation_test";
+
+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) => {
@@ -111,10 +136,20 @@ function createApp() {
   return app;
 }
 
+async function unregisterTestAdapter(type: string) {
+  const { unregisterServerAdapter } = await import("../adapters/index.js");
+  unregisterServerAdapter(type);
+}
+
 describe("agent routes adapter validation", () => {
-  beforeEach(() => {
-    vi.clearAllMocks();
-    unregisterServerAdapter("external_test");
+  beforeEach(async () => {
+    vi.resetModules();
+    vi.doUnmock("../routes/agents.js");
+    vi.doUnmock("../routes/authz.js");
+    vi.doUnmock("../middleware/index.js");
+    vi.doUnmock("../routes/agents.js");
+    registerModuleMocks();
+    vi.resetAllMocks();
     mockCompanySkillService.listRuntimeSkillEntries.mockResolvedValue([]);
     mockCompanySkillService.resolveRequestedSkillKeys.mockResolvedValue([]);
     mockAccessService.canUser.mockResolvedValue(true);
@@ -146,16 +181,21 @@ describe("agent routes adapter validation", () => {
       createdAt: new Date(),
       updatedAt: new Date(),
     }));
+    await unregisterTestAdapter("external_test");
+    await unregisterTestAdapter(missingAdapterType);
   });
 
-  afterEach(() => {
-    unregisterServerAdapter("external_test");
+  afterEach(async () => {
+    await unregisterTestAdapter("external_test");
+    await unregisterTestAdapter(missingAdapterType);
   });
 
   it("creates agents for dynamically registered external adapter types", async () => {
+    const { registerServerAdapter } = await import("../adapters/index.js");
     registerServerAdapter(externalAdapter);
 
-    const res = await request(createApp())
+    const app = await createApp();
+    const res = await request(app)
       .post("/api/companies/company-1/agents")
       .send({
         name: "External Agent",
@@ -167,14 +207,15 @@ describe("agent routes adapter validation", () => {
   });
 
   it("rejects unknown adapter types even when schema accepts arbitrary strings", async () => {
-    const res = await request(createApp())
+    const app = await createApp();
+    const res = await request(app)
       .post("/api/companies/company-1/agents")
       .send({
         name: "Missing Adapter",
-        adapterType: "missing_adapter",
+        adapterType: missingAdapterType,
       });
 
     expect(res.status, JSON.stringify(res.body)).toBe(422);
-    expect(String(res.body.error ?? res.body.message ?? "")).toContain("Unknown adapter type: missing_adapter");
+    expect(String(res.body.error ?? res.body.message ?? "")).toContain(`Unknown adapter type: ${missingAdapterType}`);
   });
 });