[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/services/company-portability.ts

@@ -31,6 +31,7 @@ import type {
   RoutineVariable,
 } from "@paperclipai/shared";
 import {
+  AGENT_DEFAULT_MAX_CONCURRENT_RUNS,
   ISSUE_PRIORITIES,
   ISSUE_STATUSES,
   PROJECT_STATUSES,
@@ -590,7 +591,7 @@ const RUNTIME_DEFAULT_RULES: Array<{ path: string[]; value: unknown }> = [
   { path: ["heartbeat", "wakeOnAssignment"], value: true },
   { path: ["heartbeat", "wakeOnAutomation"], value: true },
   { path: ["heartbeat", "wakeOnDemand"], value: true },
-  { path: ["heartbeat", "maxConcurrentRuns"], value: 3 },
+  { path: ["heartbeat", "maxConcurrentRuns"], value: AGENT_DEFAULT_MAX_CONCURRENT_RUNS },
 ];
 
 const ADAPTER_DEFAULT_RULES_BY_TYPE: Record<string, Array<{ path: string[]; value: unknown }>> = {
@@ -741,10 +742,20 @@ function clonePortableRecord(value: unknown) {
   return structuredClone(value) as Record<string, unknown>;
 }
 
+function parseFiniteNumberLike(value: unknown): number | null {
+  if (typeof value === "number" && Number.isFinite(value)) return value;
+  if (typeof value !== "string") return null;
+  const parsed = Number(value.trim());
+  return Number.isFinite(parsed) ? parsed : null;
+}
+
 function disableImportedTimerHeartbeat(runtimeConfig: unknown) {
   const next = clonePortableRecord(runtimeConfig) ?? {};
   const heartbeat = isPlainRecord(next.heartbeat) ? { ...next.heartbeat } : {};
   heartbeat.enabled = false;
+  if (parseFiniteNumberLike(heartbeat.maxConcurrentRuns) == null) {
+    heartbeat.maxConcurrentRuns = AGENT_DEFAULT_MAX_CONCURRENT_RUNS;
+  }
   next.heartbeat = heartbeat;
   return next;
 }
@@ -4209,13 +4220,7 @@ export function companyPortabilityService(db: Db, storage?: StorageService) {
           continue;
         }
 
-        const requiresApproval =
-          typeof targetCompany.requireBoardApprovalForNewAgents === "boolean"
-            ? targetCompany.requireBoardApprovalForNewAgents
-            : include.company
-              ? (sourceManifest.company?.requireBoardApprovalForNewAgents ?? true)
-              : true;
-        const createdStatus = requiresApproval ? "pending_approval" : "idle";
+        const createdStatus = "idle";
         let created = await agents.create(targetCompany.id, {
           ...patch,
           status: createdStatus,