[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/routes/execution-workspaces.ts

@@ -28,6 +28,9 @@ import {
   collectExecutionWorkspaceCommandPaths,
 } from "./workspace-command-authz.js";
 import { assertCanManageExecutionWorkspaceRuntimeServices } from "./workspace-runtime-service-authz.js";
+import { appendWithCap } from "../adapters/utils.js";
+
+const WORKSPACE_CONTROL_OUTPUT_MAX_CHARS = 256 * 1024;
 
 export function executionWorkspaceRoutes(db: Db) {
   const router = Router();
@@ -209,8 +212,8 @@ export function executionWorkspaceRoutes(db: Db) {
       executionWorkspaceId: existing.id,
     });
     let runtimeServiceCount = existing.runtimeServices?.length ?? 0;
-    const stdout: string[] = [];
-    const stderr: string[] = [];
+    let stdout = "";
+    let stderr = "";
 
     const operation = await recorder.recordOperation({
       phase: action === "stop" ? "workspace_teardown" : "workspace_provision",
@@ -310,8 +313,8 @@ export function executionWorkspaceRoutes(db: Db) {
         }
 
         const onLog = async (stream: "stdout" | "stderr", chunk: string) => {
-          if (stream === "stdout") stdout.push(chunk);
-          else stderr.push(chunk);
+          if (stream === "stdout") stdout = appendWithCap(stdout, chunk, WORKSPACE_CONTROL_OUTPUT_MAX_CHARS);
+          else stderr = appendWithCap(stderr, chunk, WORKSPACE_CONTROL_OUTPUT_MAX_CHARS);
         };
 
         if (action === "stop" || action === "restart") {
@@ -382,8 +385,8 @@ export function executionWorkspaceRoutes(db: Db) {
 
         return {
           status: "succeeded",
-          stdout: stdout.join(""),
-          stderr: stderr.join(""),
+          stdout,
+          stderr,
           system:
             action === "stop"
               ? "Stopped execution workspace runtime services.\n"