[codex] Improve agent runtime recovery and governance (#4086)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The heartbeat runtime, agent import path, and agent configuration
defaults determine whether work is dispatched safely and predictably.
> - Several accumulated fixes all touched agent execution recovery, wake
routing, import behavior, and runtime concurrency defaults.
> - Those changes need to land together so the heartbeat service and
agent creation defaults stay internally consistent.
> - This pull request groups the runtime/governance changes from the
split branch into one standalone branch.
> - The benefit is safer recovery for stranded runs, bounded high-volume
reads, imported-agent approval correctness, skill-template support, and
a clearer default concurrency policy.

## What Changed

- Fixed stranded continuation recovery so successful automatic retries
are requeued instead of incorrectly blocking the issue.
- Bounded high-volume issue/log reads across issue, heartbeat, agent,
project, and workspace paths.
- Fixed imported-agent approval and instruction-path permission
handling.
- Quarantined seeded worktree execution state during worktree
provisioning.
- Queued approval follow-up wakes and hardened SQL_ASCII heartbeat
output handling.
- Added reusable agent instruction templates for hiring flows.
- Set the default max concurrent agent runs to five and updated related
UI/tests/docs.

## Verification

- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run server/src/__tests__/company-portability.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
server/src/__tests__/heartbeat-comment-wake-batching.test.ts
server/src/__tests__/heartbeat-list.test.ts
server/src/__tests__/issues-service.test.ts
server/src/__tests__/agent-permissions-routes.test.ts
packages/adapter-utils/src/server-utils.test.ts
ui/src/lib/new-agent-runtime-config.test.ts`
- Split integration check: merged this branch first, followed by the
other [PAP-1614](/PAP/issues/PAP-1614) branches, with no merge
conflicts.
- Confirmed this branch does not include `pnpm-lock.yaml`.

## Risks

- Medium risk: touches heartbeat recovery, queueing, and issue list
bounds in central runtime paths.
- Imported-agent and concurrency default behavior changes may affect
existing automation that assumes one-at-a-time default runs.
- No database migrations are included.

> 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 tool-enabled coding model, agentic
code-editing/runtime with local shell and GitHub CLI access; exact
context window and reasoning mode are not exposed by the Paperclip
harness.

## 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

---------

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

server/src/__tests__/heartbeat-comment-wake-batching.test.ts

@@ -236,6 +236,115 @@ describe("heartbeat comment wake batching", () => {
     }
   });
 
+  it("defers approval-approved wakes for a running issue so the assignee resumes after the run", async () => {
+    const companyId = randomUUID();
+    const agentId = randomUUID();
+    const issueId = randomUUID();
+    const runId = randomUUID();
+    const issuePrefix = `T${companyId.replace(/-/g, "").slice(0, 6).toUpperCase()}`;
+    const heartbeat = heartbeatService(db);
+
+    await db.insert(companies).values({
+      id: companyId,
+      name: "Paperclip",
+      issuePrefix,
+      requireBoardApprovalForNewAgents: false,
+    });
+
+    await db.insert(agents).values({
+      id: agentId,
+      companyId,
+      name: "CEO",
+      role: "ceo",
+      status: "running",
+      adapterType: "process",
+      adapterConfig: {},
+      runtimeConfig: {},
+      permissions: {},
+    });
+
+    await db.insert(heartbeatRuns).values({
+      id: runId,
+      companyId,
+      agentId,
+      invocationSource: "assignment",
+      triggerDetail: "system",
+      status: "running",
+      contextSnapshot: {
+        issueId,
+        taskId: issueId,
+        wakeReason: "issue_assigned",
+      },
+    });
+
+    await db.insert(issues).values({
+      id: issueId,
+      companyId,
+      title: "Hire an agent",
+      status: "blocked",
+      priority: "medium",
+      assigneeAgentId: agentId,
+      executionRunId: runId,
+      executionAgentNameKey: "ceo",
+      executionLockedAt: new Date(),
+      issueNumber: 1,
+      identifier: `${issuePrefix}-1`,
+    });
+
+    const followupRun = await heartbeat.wakeup(agentId, {
+      source: "automation",
+      triggerDetail: "system",
+      reason: "approval_approved",
+      payload: {
+        issueId,
+        approvalId: "approval-1",
+        approvalStatus: "approved",
+      },
+      contextSnapshot: {
+        issueId,
+        taskId: issueId,
+        approvalId: "approval-1",
+        approvalStatus: "approved",
+        wakeReason: "approval_approved",
+      },
+      requestedByActorType: "user",
+      requestedByActorId: "local-board",
+    });
+
+    expect(followupRun).toBeNull();
+
+    const deferred = await db
+      .select()
+      .from(agentWakeupRequests)
+      .where(
+        and(
+          eq(agentWakeupRequests.companyId, companyId),
+          eq(agentWakeupRequests.agentId, agentId),
+          eq(agentWakeupRequests.status, "deferred_issue_execution"),
+        ),
+      )
+      .then((rows) => rows[0] ?? null);
+
+    expect(deferred).not.toBeNull();
+    expect(deferred?.reason).toBe("issue_execution_deferred");
+    expect(deferred?.payload).toMatchObject({
+      issueId,
+      approvalId: "approval-1",
+      approvalStatus: "approved",
+    });
+    expect((deferred?.payload as Record<string, unknown>)._paperclipWakeContext).toMatchObject({
+      issueId,
+      taskId: issueId,
+      approvalId: "approval-1",
+      approvalStatus: "approved",
+      wakeReason: "approval_approved",
+    });
+
+    const runs = await db.select().from(heartbeatRuns).where(eq(heartbeatRuns.agentId, agentId));
+    expect(runs).toHaveLength(1);
+    expect(runs[0]?.id).toBe(runId);
+  });
+
   it("batches deferred comment wakes and forwards the ordered batch to the next run", async () => {
     const gateway = await createControlledGatewayServer();
     const companyId = randomUUID();