[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/workspace-runtime.ts

@@ -413,32 +413,33 @@ function formatCommandForDisplay(command: string, args: string[]) {
     .join(" ");
 }
 
+function trimToLastBytes(value: string, limit: number) {
+  const byteLength = Buffer.byteLength(value, "utf8");
+  if (byteLength <= limit) return value;
+  return Buffer.from(value, "utf8").subarray(byteLength - limit).toString("utf8");
+}
+
 function createProcessOutputCapture(maxBytes: number): ProcessOutputAccumulator {
   const limit = Math.max(1, Math.trunc(maxBytes));
-  let chunks: string[] = [];
+  let text = "";
   let truncated = false;
   let totalBytes = 0;
 
   return {
     append(chunk: string) {
       if (!chunk) return;
-      chunks.push(chunk);
       totalBytes += Buffer.byteLength(chunk, "utf8");
 
-      let currentBytes = chunks.reduce((sum, value) => sum + Buffer.byteLength(value, "utf8"), 0);
-      if (currentBytes <= limit) return;
-
-      const combined = Buffer.from(chunks.join(""), "utf8");
-      const tail = combined.subarray(Math.max(0, combined.length - limit)).toString("utf8");
-      chunks = [tail];
-      truncated = true;
-      currentBytes = Buffer.byteLength(tail, "utf8");
-      if (currentBytes > limit) {
-        chunks = [Buffer.from(tail, "utf8").subarray(Math.max(0, currentBytes - limit)).toString("utf8")];
+      const combined = text + chunk;
+      if (Buffer.byteLength(combined, "utf8") <= limit) {
+        text = combined;
+        return;
       }
+
+      text = trimToLastBytes(combined, limit);
+      truncated = true;
     },
     finish(): ProcessOutputCapture {
-      const text = chunks.join("");
       if (!truncated) {
         return {
           text,