[codex] Harden heartbeat scheduling and runtime controls (#4223)

## Thinking Path

> - Paperclip orchestrates AI agents through issue checkout, heartbeat
runs, routines, and auditable control-plane state
> - The runtime path has to recover from lost local processes, transient
adapter failures, blocked dependencies, and routine coalescing without
stranding work
> - The existing branch carried several reliability fixes across
heartbeat scheduling, issue runtime controls, routine dispatch, and
operator-facing run state
> - These changes belong together because they share backend contracts,
migrations, and runtime status semantics
> - This pull request groups the control-plane/runtime slice so it can
merge independently from board UI polish and adapter sandbox work
> - The benefit is safer heartbeat recovery, clearer runtime controls,
and more predictable recurring execution behavior

## What Changed

- Adds bounded heartbeat retry scheduling, scheduled retry state, and
Codex transient failure recovery handling.
- Tightens heartbeat process recovery, blocker wake behavior, issue
comment wake handling, routine dispatch coalescing, and
activity/dashboard bounds.
- Adds runtime-control MCP tools and Paperclip skill docs for issue
workspace runtime management.
- Adds migrations `0061_lively_thor_girl.sql` and
`0062_routine_run_dispatch_fingerprint.sql`.
- Surfaces retry state in run ledger/agent UI and keeps related shared
types synchronized.

## Verification

- `pnpm exec vitest run
server/src/__tests__/heartbeat-retry-scheduling.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/routines-service.test.ts`
- `pnpm exec vitest run src/tools.test.ts` from `packages/mcp-server`

## Risks

- Medium risk: this touches heartbeat recovery and routine dispatch,
which are central execution paths.
- Migration order matters if split branches land out of order: merge
this PR before branches that assume the new runtime/routine fields.
- Runtime retry behavior should be watched in CI and in local operator
smoke tests because it changes how transient failures are resumed.

> 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-based coding agent runtime, shell/git tool use
enabled. Exact hosted model build and context window are not exposed in
this Paperclip heartbeat environment.

## 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
- [ ] 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

server/src/__tests__/activity-routes.test.ts

@@ -21,6 +21,10 @@ const mockIssueService = vi.hoisted(() => ({
 
 vi.mock("../services/activity.js", () => ({
   activityService: () => mockActivityService,
+  normalizeActivityLimit: (limit: number | undefined) => {
+    if (!Number.isFinite(limit)) return 100;
+    return Math.max(1, Math.min(500, Math.floor(limit ?? 100)));
+  },
 }));
 
 vi.mock("../services/index.js", () => ({
@@ -58,6 +62,38 @@ describe("activity routes", () => {
     vi.clearAllMocks();
   });
 
+  it("limits company activity lists by default", async () => {
+    mockActivityService.list.mockResolvedValue([]);
+
+    const app = await createApp();
+    const res = await request(app).get("/api/companies/company-1/activity");
+
+    expect(res.status).toBe(200);
+    expect(mockActivityService.list).toHaveBeenCalledWith({
+      companyId: "company-1",
+      agentId: undefined,
+      entityType: undefined,
+      entityId: undefined,
+      limit: 100,
+    });
+  });
+
+  it("caps requested company activity list limits", async () => {
+    mockActivityService.list.mockResolvedValue([]);
+
+    const app = await createApp();
+    const res = await request(app).get("/api/companies/company-1/activity?limit=5000&entityType=issue");
+
+    expect(res.status).toBe(200);
+    expect(mockActivityService.list).toHaveBeenCalledWith({
+      companyId: "company-1",
+      agentId: undefined,
+      entityType: "issue",
+      entityId: undefined,
+      limit: 500,
+    });
+  });
+
   it("resolves issue identifiers before loading runs", async () => {
     mockIssueService.getByIdentifier.mockResolvedValue({
       id: "issue-uuid-1",