[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__/health.test.ts

@@ -3,10 +3,25 @@ import express from "express";
 import request from "supertest";
 import type { Db } from "@paperclipai/db";
 import { serverVersion } from "../version.js";
+import { healthRoutes } from "../routes/health.js";
+
+const mockReadPersistedDevServerStatus = vi.hoisted(() => vi.fn());
+
+vi.mock("../dev-server-status.js", () => ({
+  readPersistedDevServerStatus: mockReadPersistedDevServerStatus,
+  toDevServerHealthStatus: vi.fn(),
+}));
+
+function createApp(db?: Db) {
+  const app = express();
+  app.use("/health", healthRoutes(db));
+  return app;
+}
 
 describe("GET /health", () => {
   beforeEach(() => {
-    vi.resetModules();
+    vi.clearAllMocks();
+    mockReadPersistedDevServerStatus.mockReturnValue(undefined);
   });
 
   afterEach(() => {
@@ -14,11 +29,7 @@ describe("GET /health", () => {
   });
 
   it("returns 200 with status ok", async () => {
-    const devServerStatus = await import("../dev-server-status.js");
-    vi.spyOn(devServerStatus, "readPersistedDevServerStatus").mockReturnValue(undefined);
-    const { healthRoutes } = await import("../routes/health.js");
-    const app = express();
-    app.use("/health", healthRoutes());
+    const app = createApp();
 
     const res = await request(app).get("/health");
     expect(res.status).toBe(200);
@@ -26,14 +37,10 @@ describe("GET /health", () => {
   });
 
   it("returns 200 when the database probe succeeds", async () => {
-    const devServerStatus = await import("../dev-server-status.js");
-    vi.spyOn(devServerStatus, "readPersistedDevServerStatus").mockReturnValue(undefined);
-    const { healthRoutes } = await import("../routes/health.js");
     const db = {
       execute: vi.fn().mockResolvedValue([{ "?column?": 1 }]),
     } as unknown as Db;
-    const app = express();
-    app.use("/health", healthRoutes(db));
+    const app = createApp(db);
 
     const res = await request(app).get("/health");
 
@@ -42,14 +49,10 @@ describe("GET /health", () => {
   });
 
   it("returns 503 when the database probe fails", async () => {
-    const devServerStatus = await import("../dev-server-status.js");
-    vi.spyOn(devServerStatus, "readPersistedDevServerStatus").mockReturnValue(undefined);
-    const { healthRoutes } = await import("../routes/health.js");
     const db = {
       execute: vi.fn().mockRejectedValue(new Error("connect ECONNREFUSED")),
     } as unknown as Db;
-    const app = express();
-    app.use("/health", healthRoutes(db));
+    const app = createApp(db);
 
     const res = await request(app).get("/health");