[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/app.ts

@@ -50,9 +50,27 @@ import { createPluginHostServiceCleanup } from "./services/plugin-host-service-c
 import { pluginRegistryService } from "./services/plugin-registry.js";
 import { createHostClientHandlers } from "@paperclipai/plugin-sdk";
 import type { BetterAuthSessionResult } from "./auth/better-auth.js";
+import { createCachedViteHtmlRenderer } from "./vite-html-renderer.js";
 
 type UiMode = "none" | "static" | "vite-dev";
 const FEEDBACK_EXPORT_FLUSH_INTERVAL_MS = 5_000;
+const VITE_DEV_ASSET_PREFIXES = [
+  "/@fs/",
+  "/@id/",
+  "/@react-refresh",
+  "/@vite/",
+  "/assets/",
+  "/node_modules/",
+  "/src/",
+];
+const VITE_DEV_STATIC_PATHS = new Set([
+  "/apple-touch-icon.png",
+  "/favicon-16x16.png",
+  "/favicon-32x32.png",
+  "/favicon.ico",
+  "/favicon.svg",
+  "/site.webmanifest",
+]);
 
 export function resolveViteHmrPort(serverPort: number): number {
   if (serverPort <= 55_535) {
@@ -61,6 +79,13 @@ export function resolveViteHmrPort(serverPort: number): number {
   return Math.max(1_024, serverPort - 10_000);
 }
 
+function shouldServeViteDevHtml(req: ExpressRequest): boolean {
+  const pathname = req.path;
+  if (VITE_DEV_STATIC_PATHS.has(pathname)) return false;
+  if (VITE_DEV_ASSET_PREFIXES.some((prefix) => pathname.startsWith(prefix))) return false;
+  return req.accepts(["html"]) === "html";
+}
+
 export async function createApp(
   db: Db,
   opts: {
@@ -195,6 +220,7 @@ export async function createApp(
     jobStore,
   });
   const hostServiceCleanup = createPluginHostServiceCleanup(lifecycle, hostServicesDisposers);
+  let viteHtmlRenderer: ReturnType<typeof createCachedViteHtmlRenderer> | null = null;
   const loader = pluginLoader(
     db,
     { localPluginDir: opts.localPluginDir ?? DEFAULT_LOCAL_PLUGIN_DIR },
@@ -287,18 +313,26 @@ export async function createApp(
         allowedHosts: privateHostnameGateEnabled ? Array.from(privateHostnameAllowSet) : undefined,
       },
     });
+    viteHtmlRenderer = createCachedViteHtmlRenderer({
+      vite,
+      uiRoot,
+      brandHtml: applyUiBranding,
+    });
+    const renderViteHtml = viteHtmlRenderer;
 
-    app.use(vite.middlewares);
     app.get(/.*/, async (req, res, next) => {
+      if (!shouldServeViteDevHtml(req)) {
+        next();
+        return;
+      }
       try {
-        const templatePath = path.resolve(uiRoot, "index.html");
-        const template = fs.readFileSync(templatePath, "utf-8");
-        const html = applyUiBranding(await vite.transformIndexHtml(req.originalUrl, template));
+        const html = await renderViteHtml.render(req.originalUrl);
         res.status(200).set({ "Content-Type": "text/html" }).end(html);
       } catch (err) {
         next(err);
       }
     });
+    app.use(vite.middlewares);
   }
 
   app.use(errorHandler);
@@ -340,6 +374,7 @@ export async function createApp(
   process.once("exit", () => {
     if (feedbackExportTimer) clearInterval(feedbackExportTimer);
     devWatcher?.close();
+    viteHtmlRenderer?.dispose();
     hostServiceCleanup.disposeAll();
     hostServiceCleanup.teardown();
   });