[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/middleware/http-log-policy.ts

@@ -0,0 +1,47 @@
+const SILENCED_SUCCESS_METHODS = new Set(["GET", "HEAD"]);
+
+const SILENCED_SUCCESS_API_PATHS = [
+  /^\/api\/health(?:\/|$)/,
+  /^\/api\/companies\/[^/]+\/activity(?:\/|$)/,
+  /^\/api\/companies\/[^/]+\/dashboard(?:\/|$)/,
+  /^\/api\/companies\/[^/]+\/heartbeat-runs(?:\/|$)/,
+  /^\/api\/companies\/[^/]+\/issues(?:\/|$)/,
+  /^\/api\/companies\/[^/]+\/live-runs(?:\/|$)/,
+  /^\/api\/companies\/[^/]+\/sidebar-badges(?:\/|$)/,
+  /^\/api\/heartbeat-runs\/[^/]+\/log(?:\/|$)/,
+];
+
+const SILENCED_SUCCESS_STATIC_PREFIXES = [
+  "/@fs/",
+  "/@id/",
+  "/@react-refresh",
+  "/@vite/",
+  "/_plugins/",
+  "/assets/",
+  "/node_modules/",
+  "/src/",
+];
+
+const SILENCED_SUCCESS_STATIC_PATHS = new Set([
+  "/favicon.ico",
+  "/site.webmanifest",
+]);
+
+function normalizePath(url: string): string {
+  const trimmed = url.trim();
+  if (trimmed.length === 0) return "/";
+  const pathname = trimmed.split("?")[0]?.trim() ?? "/";
+  return pathname.length > 0 ? pathname : "/";
+}
+
+export function shouldSilenceHttpSuccessLog(method: string | undefined, url: string | undefined, statusCode: number): boolean {
+  if (statusCode >= 400) return false;
+  if (statusCode === 304) return true;
+  if (!method || !url) return false;
+  if (!SILENCED_SUCCESS_METHODS.has(method.toUpperCase())) return false;
+
+  const pathname = normalizePath(url);
+  if (SILENCED_SUCCESS_STATIC_PATHS.has(pathname)) return true;
+  if (SILENCED_SUCCESS_STATIC_PREFIXES.some((prefix) => pathname.startsWith(prefix))) return true;
+  return SILENCED_SUCCESS_API_PATHS.some((pattern) => pattern.test(pathname));
+}

server/src/middleware/logger.ts

@@ -4,6 +4,7 @@ import pino from "pino";
 import { pinoHttp } from "pino-http";
 import { readConfigFile } from "../config-file.js";
 import { resolveDefaultLogsDir, resolveHomeAwarePath } from "../home-paths.js";
+import { shouldSilenceHttpSuccessLog } from "./http-log-policy.js";
 
 function resolveServerLogDir(): string {
   const envOverride = process.env.PAPERCLIP_LOG_DIR?.trim();
@@ -47,6 +48,9 @@ export const logger = pino({
 export const httpLogger = pinoHttp({
   logger,
   customLogLevel(_req, res, err) {
+    if (shouldSilenceHttpSuccessLog(_req.method, _req.url, res.statusCode)) {
+      return "silent";
+    }
     if (err || res.statusCode >= 500) return "error";
     if (res.statusCode >= 400) return "warn";
     return "info";