[codex] Add run liveness continuations (#4083)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - Heartbeat runs are the control-plane record of each agent execution
window.
> - Long-running local agents can exhaust context or stop while still
holding useful next-step state.
> - Operators need that stop reason, next action, and continuation path
to be durable and visible.
> - This pull request adds run liveness metadata, continuation
summaries, and UI surfaces for issue run ledgers.
> - The benefit is that interrupted or long-running work can resume with
clearer context instead of losing the agent's last useful handoff.

## What Changed

- Added heartbeat-run liveness fields, continuation attempt tracking,
and an idempotent `0058` migration.
- Added server services and tests for run liveness, continuation
summaries, stop metadata, and activity backfill.
- Wired local and HTTP adapters to surface continuation/liveness context
through shared adapter utilities.
- Added shared constants, validators, and heartbeat types for liveness
continuation state.
- Added issue-detail UI surfaces for continuation handoffs and the run
ledger, with component tests.
- Updated agent runtime docs, heartbeat protocol docs, prompt guidance,
onboarding assets, and skills instructions to explain continuation
behavior.
- Addressed Greptile feedback by scoping document evidence by run,
excluding system continuation-summary documents from liveness evidence,
importing shared liveness types, surfacing hidden ledger run counts,
documenting bounded retry behavior, and moving run-ledger liveness
backfill off the request path.

## Verification

- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
server/src/__tests__/run-continuations.test.ts
server/src/__tests__/run-liveness.test.ts
server/src/__tests__/activity-service.test.ts
server/src/__tests__/documents-service.test.ts
server/src/__tests__/issue-continuation-summary.test.ts
server/src/services/heartbeat-stop-metadata.test.ts
ui/src/components/IssueRunLedger.test.tsx
ui/src/components/IssueContinuationHandoff.test.tsx
ui/src/components/IssueDocumentsSection.test.tsx`
- `pnpm --filter @paperclipai/db build`
- `pnpm exec vitest run server/src/__tests__/activity-service.test.ts
ui/src/components/IssueRunLedger.test.tsx`
- `pnpm --filter @paperclipai/ui typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run server/src/__tests__/activity-service.test.ts
server/src/__tests__/run-continuations.test.ts
ui/src/components/IssueRunLedger.test.tsx`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "treats a
plan document update"`
- `pnpm exec vitest run server/src/__tests__/activity-service.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts -t "activity
service|treats a plan document update"`
- Remote PR checks on head `e53b1a1d`: `verify`, `e2e`, `policy`, and
Snyk all passed.
- Confirmed `public-gh/master` is an ancestor of this branch after
fetching `public-gh master`.
- Confirmed `pnpm-lock.yaml` is not included in the branch diff.
- Confirmed migration `0058_wealthy_starbolt.sql` is ordered after
`0057` and uses `IF NOT EXISTS` guards for repeat application.
- Greptile inline review threads are resolved.

## Risks

- Medium risk: this touches heartbeat execution, liveness recovery,
activity rendering, issue routes, shared contracts, docs, and UI.
- Migration risk is mitigated by additive columns/indexes and idempotent
guards.
- Run-ledger liveness backfill is now asynchronous, so the first ledger
response can briefly show historical missing liveness until the
background backfill completes.
- UI screenshot coverage is not included in this packaging pass;
validation is currently through focused component tests.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5.4, local tool-use coding agent with terminal, git,
GitHub connector, GitHub CLI, and Paperclip API access.

## 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)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] 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

Screenshot note: no before/after screenshots were captured in this PR
packaging pass; the UI changes are covered by focused component tests
listed above.

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

server/src/adapters/http/execute.test.ts

@@ -0,0 +1,46 @@
+import { afterEach, describe, expect, it, vi } from "vitest";
+import { execute } from "./execute.js";
+
+afterEach(() => {
+  vi.unstubAllGlobals();
+});
+
+describe("http adapter execute", () => {
+  it("reports configured request timeout as timed_out", async () => {
+    vi.stubGlobal(
+      "fetch",
+      vi.fn((_url: string, init?: RequestInit) => new Promise((_resolve, reject) => {
+        init?.signal?.addEventListener("abort", () => {
+          reject(new DOMException("Aborted", "AbortError"));
+        });
+      })),
+    );
+
+    const result = await execute({
+      runId: "run-1",
+      agent: {
+        id: "agent-1",
+        companyId: "company-1",
+        name: "Agent",
+        adapterType: "http",
+        adapterConfig: {},
+      },
+      runtime: {
+        sessionId: null,
+        sessionParams: null,
+        sessionDisplayId: null,
+        taskKey: null,
+      },
+      config: {
+        url: "https://example.test/webhook",
+        timeoutMs: 1,
+      },
+      context: {},
+      onLog: async () => {},
+    });
+
+    expect(result.timedOut).toBe(true);
+    expect(result.errorCode).toBe("timeout");
+    expect(result.errorMessage).toContain("timed out after 1ms");
+  });
+});

server/src/adapters/http/execute.ts

@@ -36,6 +36,17 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
       timedOut: false,
       summary: `HTTP ${method} ${url}`,
     };
+  } catch (err) {
+    if (timer && err instanceof Error && err.name === "AbortError") {
+      return {
+        exitCode: null,
+        signal: null,
+        timedOut: true,
+        errorMessage: `HTTP ${method} ${url} timed out after ${timeoutMs}ms`,
+        errorCode: "timeout",
+      };
+    }
+    throw err;
   } finally {
     if (timer) clearTimeout(timer);
   }