[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__/vite-html-renderer.test.ts

@@ -0,0 +1,91 @@
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import { createCachedViteHtmlRenderer, type ViteWatcherHost } from "../vite-html-renderer.js";
+
+function createWatcher() {
+  const listeners = new Map<string, Set<(file: string) => void>>();
+
+  return {
+    on(event: string, listener: (file: string) => void) {
+      if (!listeners.has(event)) listeners.set(event, new Set());
+      listeners.get(event)?.add(listener);
+    },
+    off(event: string, listener: (file: string) => void) {
+      listeners.get(event)?.delete(listener);
+    },
+    emit(event: string, file: string) {
+      for (const listener of listeners.get(event) ?? []) {
+        listener(file);
+      }
+    },
+  };
+}
+
+describe("createCachedViteHtmlRenderer", () => {
+  const tempDirs: string[] = [];
+
+  afterEach(() => {
+    for (const dir of tempDirs.splice(0)) {
+      fs.rmSync(dir, { recursive: true, force: true });
+    }
+  });
+
+  it("reuses the injected dev html shell until a watched file changes", async () => {
+    const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-vite-html-"));
+    tempDirs.push(tempDir);
+    const indexPath = path.join(tempDir, "index.html");
+    fs.writeFileSync(
+      indexPath,
+      '<html><body>v1<script type="module" src="/src/main.tsx"></script></body></html>',
+      "utf8",
+    );
+
+    const watcher = createWatcher();
+    const vite: ViteWatcherHost = {
+      watcher,
+    };
+
+    const renderer = createCachedViteHtmlRenderer({ vite, uiRoot: tempDir });
+
+    await expect(renderer.render("/")).resolves.toContain("/@vite/client");
+    await expect(renderer.render("/")).resolves.toContain('"/@react-refresh"');
+    const first = await renderer.render("/");
+    const second = await renderer.render("/issues");
+    expect(first).toBe(second);
+    expect(first.match(/\/@vite\/client/g)?.length).toBe(1);
+    expect(first).toContain("window.$RefreshReg$");
+
+    fs.writeFileSync(
+      indexPath,
+      '<html><body>v2<script type="module" src="/src/main.tsx"></script></body></html>',
+      "utf8",
+    );
+    watcher.emit("change", indexPath);
+
+    await expect(renderer.render("/")).resolves.toContain("v2");
+
+    renderer.dispose();
+  });
+
+  it("does not duplicate the vite client tag or react refresh preamble when already present", async () => {
+    const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-vite-html-"));
+    tempDirs.push(tempDir);
+    fs.writeFileSync(
+      path.join(tempDir, "index.html"),
+      '<html><head><script type="module">import { injectIntoGlobalHook } from "/@react-refresh";injectIntoGlobalHook(window);window.$RefreshReg$ = () => {};window.$RefreshSig$ = () => (type) => type;</script></head><body><script type="module" src="/@vite/client"></script><script type="module" src="/src/main.tsx"></script></body></html>',
+      "utf8",
+    );
+
+    const vite: ViteWatcherHost = {
+      watcher: createWatcher(),
+    };
+
+    const renderer = createCachedViteHtmlRenderer({ vite, uiRoot: tempDir });
+
+    const html = await renderer.render("/");
+    expect(html.match(/\/@vite\/client/g)?.length).toBe(1);
+    expect(html.match(/\/@react-refresh/g)?.length).toBe(1);
+  });
+});