[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__/heartbeat-project-env.test.ts

@@ -1,5 +1,10 @@
 import { describe, expect, it, vi } from "vitest";
-import { resolveExecutionRunAdapterConfig } from "../services/heartbeat.ts";
+import { buildSkillMentionHref } from "@paperclipai/shared";
+import {
+  applyRunScopedMentionedSkillKeys,
+  extractMentionedSkillIdsFromSources,
+  resolveExecutionRunAdapterConfig,
+} from "../services/heartbeat.ts";
 
 describe("resolveExecutionRunAdapterConfig", () => {
   it("overlays project env on top of agent env and unions secret keys", async () => {
@@ -63,3 +68,51 @@ describe("resolveExecutionRunAdapterConfig", () => {
     expect(resolveEnvBindings).not.toHaveBeenCalled();
   });
 });
+
+describe("extractMentionedSkillIdsFromSources", () => {
+  it("collects explicit skill mention ids across issue sources", () => {
+    const releaseHref = buildSkillMentionHref("skill-1", "release-changelog");
+    const browserHref = buildSkillMentionHref("skill-2", "agent-browser");
+
+    expect(
+      extractMentionedSkillIdsFromSources([
+        `Please use [/release-changelog](${releaseHref})`,
+        `And also [/agent-browser](${browserHref})`,
+        `Duplicate mention [/release-changelog](${releaseHref})`,
+      ]),
+    ).toEqual(["skill-1", "skill-2"]);
+  });
+});
+
+describe("applyRunScopedMentionedSkillKeys", () => {
+  it("adds mentioned skills without mutating the original config", () => {
+    const originalConfig = {
+      command: "codex",
+      paperclipSkillSync: {
+        desiredSkills: ["paperclipai/paperclip/paperclip"],
+      },
+    };
+
+    const updatedConfig = applyRunScopedMentionedSkillKeys(originalConfig, [
+      "company/company-1/release-changelog",
+      "paperclipai/paperclip/paperclip",
+      "company/company-1/release-changelog",
+    ]);
+
+    expect(updatedConfig).toEqual({
+      command: "codex",
+      paperclipSkillSync: {
+        desiredSkills: [
+          "paperclipai/paperclip/paperclip",
+          "company/company-1/release-changelog",
+        ],
+      },
+    });
+    expect(originalConfig).toEqual({
+      command: "codex",
+      paperclipSkillSync: {
+        desiredSkills: ["paperclipai/paperclip/paperclip"],
+      },
+    });
+  });
+});