[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__/company-portability.test.ts

@@ -2283,6 +2283,72 @@ describe("company portability", () => {
     expect(materializedFiles["AGENTS.md"]).not.toContain('name: "ClaudeCoder"');
   });
 
+  it("preserves issue labelIds through export and import round-trip", async () => {
+    const portability = companyPortabilityService({} as any);
+
+    projectSvc.list.mockResolvedValue([
+      {
+        id: "project-1",
+        name: "Launch",
+        urlKey: "launch",
+        description: null,
+        status: "active",
+        leadAgentId: null,
+        metadata: null,
+        defaultProjectWorkspaceId: null,
+      },
+    ]);
+    projectSvc.listWorkspaces.mockResolvedValue([]);
+    issueSvc.list.mockResolvedValue([
+      {
+        id: "issue-1",
+        identifier: "PAP-1",
+        title: "Labelled task",
+        description: "Has labels",
+        projectId: "project-1",
+        projectWorkspaceId: null,
+        assigneeAgentId: null,
+        status: "todo",
+        priority: "high",
+        labelIds: ["label-a", "label-b"],
+        billingCode: null,
+        executionWorkspaceSettings: null,
+        assigneeAdapterOverrides: null,
+      },
+    ]);
+
+    const exported = await portability.exportBundle("company-1", {
+      include: { company: true, agents: false, projects: true, issues: true },
+    });
+
+    const extension = asTextFile(exported.files[".paperclip.yaml"]);
+    expect(extension).toContain("labelIds:");
+    expect(extension).toContain("label-a");
+    expect(extension).toContain("label-b");
+
+    companySvc.create.mockResolvedValue({ id: "company-imported", name: "Imported" });
+    accessSvc.ensureMembership.mockResolvedValue(undefined);
+    agentSvc.list.mockResolvedValue([]);
+    projectSvc.list.mockResolvedValue([]);
+    projectSvc.create.mockResolvedValue({ id: "project-imported", name: "Launch", urlKey: "launch" });
+    issueSvc.create.mockResolvedValue({ id: "issue-imported", title: "Labelled task" });
+
+    await portability.importBundle({
+      source: { type: "inline", rootPath: exported.rootPath, files: exported.files },
+      include: { company: true, agents: false, projects: true, issues: true },
+      target: { mode: "new_company", newCompanyName: "Imported" },
+      agents: "all",
+      collisionStrategy: "rename",
+    }, "user-1");
+
+    expect(issueSvc.create).toHaveBeenCalledWith(
+      "company-imported",
+      expect.objectContaining({
+        labelIds: ["label-a", "label-b"],
+      }),
+    );
+  });
+
   it("strips root AGENTS frontmatter when importing a nested agent entry path", async () => {
     const portability = companyPortabilityService({} as any);