[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>

ui/src/components/transcript/useLiveRunTranscripts.ts

@@ -1,6 +1,7 @@
 import { useEffect, useMemo, useRef, useState } from "react";
 import { useQuery } from "@tanstack/react-query";
 import type { LiveEvent } from "@paperclipai/shared";
+import { ApiError } from "../../api/client";
 import { instanceSettingsApi } from "../../api/instanceSettings";
 import { heartbeatsApi } from "../../api/heartbeats";
 import { buildTranscript, getUIAdapter, onAdapterChange, type RunLogChunk, type TranscriptEntry } from "../../adapters";
@@ -85,6 +86,7 @@ export function useLiveRunTranscripts({
   const seenChunkKeysRef = useRef(new Set<string>());
   const pendingLogRowsByRunRef = useRef(new Map<string, string>());
   const logOffsetByRunRef = useRef(new Map<string, number>());
+  const missingTerminalLogRunIdsRef = useRef(new Set<string>());
   // Tick counter to force transcript recomputation when dynamic parser loads
   const [parserTick, setParserTick] = useState(0);
   useEffect(() => {
@@ -160,6 +162,11 @@ export function useLiveRunTranscripts({
         logOffsetByRunRef.current.delete(runId);
       }
     }
+    for (const runId of missingTerminalLogRunIdsRef.current.keys()) {
+      if (!knownRunIds.has(runId)) {
+        missingTerminalLogRunIdsRef.current.delete(runId);
+      }
+    }
   }, [normalizedRuns]);
 
   useEffect(() => {
@@ -168,6 +175,9 @@ export function useLiveRunTranscripts({
     let cancelled = false;
 
     const readRunLog = async (run: RunTranscriptSource) => {
+      if (missingTerminalLogRunIdsRef.current.has(run.id)) {
+        return;
+      }
       const offset = logOffsetByRunRef.current.get(run.id) ?? 0;
       try {
         const result = await heartbeatsApi.log(run.id, offset, LOG_READ_LIMIT_BYTES);
@@ -182,8 +192,10 @@ export function useLiveRunTranscripts({
         if (result.content.length > 0) {
           logOffsetByRunRef.current.set(run.id, offset + result.content.length);
         }
-      } catch {
-        // Ignore log read errors while output is initializing.
+      } catch (error) {
+        if (error instanceof ApiError && error.status === 404 && isTerminalStatus(run.status)) {
+          missingTerminalLogRunIdsRef.current.add(run.id);
+        }
       } finally {
         if (!cancelled) {
           setHydratedRunIds((prev) => {