[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>

ui/src/api/agents.ts

@@ -146,6 +146,7 @@ export const agentsApi = {
     ),
   pause: (id: string, companyId?: string) => api.post<Agent>(agentPath(id, companyId, "/pause"), {}),
   resume: (id: string, companyId?: string) => api.post<Agent>(agentPath(id, companyId, "/resume"), {}),
+  approve: (id: string, companyId?: string) => api.post<Agent>(agentPath(id, companyId, "/approve"), {}),
   terminate: (id: string, companyId?: string) => api.post<Agent>(agentPath(id, companyId, "/terminate"), {}),
   remove: (id: string, companyId?: string) => api.delete<{ ok: true }>(agentPath(id, companyId)),
   listKeys: (id: string, companyId?: string) => api.get<AgentKey[]>(agentPath(id, companyId, "/keys")),

ui/src/components/AgentConfigForm.tsx

@@ -6,6 +6,7 @@ import type {
   CompanySecret,
   EnvBinding,
 } from "@paperclipai/shared";
+import { AGENT_DEFAULT_MAX_CONCURRENT_RUNS } from "@paperclipai/shared";
 import type { AdapterModel } from "../api/agents";
 import { agentsApi } from "../api/agents";
 import { secretsApi } from "../api/secrets";
@@ -921,7 +922,7 @@ export function AgentConfigForm(props: AgentConfigFormProps) {
                   value={eff(
                     "heartbeat",
                     "maxConcurrentRuns",
-                    Number(heartbeat.maxConcurrentRuns ?? 1),
+                    Number(heartbeat.maxConcurrentRuns ?? AGENT_DEFAULT_MAX_CONCURRENT_RUNS),
                   )}
                   onCommit={(v) => mark("heartbeat", "maxConcurrentRuns", v)}
                   immediate

ui/src/hooks/useInboxBadge.ts

@@ -21,6 +21,7 @@ import {
 } from "../lib/inbox";
 
 const INBOX_ISSUE_STATUSES = "backlog,todo,in_progress,in_review,blocked,done";
+const INBOX_BADGE_ISSUE_LIMIT = 500;
 const INBOX_BADGE_HEARTBEAT_RUN_LIMIT = 200;
 
 export function useDismissedInboxAlerts() {
@@ -180,6 +181,7 @@ export function useInboxBadge(companyId: string | null | undefined) {
         touchedByUserId: "me",
         inboxArchivedByUserId: "me",
         status: INBOX_ISSUE_STATUSES,
+        limit: INBOX_BADGE_ISSUE_LIMIT,
       }),
     enabled: !!companyId,
   });

ui/src/lib/new-agent-runtime-config.test.ts

@@ -10,7 +10,7 @@ describe("buildNewAgentRuntimeConfig", () => {
         intervalSec: 300,
         wakeOnDemand: true,
         cooldownSec: 10,
-        maxConcurrentRuns: 1,
+        maxConcurrentRuns: 5,
       },
     });
   });
@@ -27,7 +27,7 @@ describe("buildNewAgentRuntimeConfig", () => {
         intervalSec: 3600,
         wakeOnDemand: true,
         cooldownSec: 10,
-        maxConcurrentRuns: 1,
+        maxConcurrentRuns: 5,
       },
     });
   });

ui/src/lib/new-agent-runtime-config.ts

@@ -1,3 +1,4 @@
+import { AGENT_DEFAULT_MAX_CONCURRENT_RUNS } from "@paperclipai/shared";
 import { defaultCreateValues } from "../components/agent-config-defaults";
 
 export function buildNewAgentRuntimeConfig(input?: {
@@ -10,7 +11,7 @@ export function buildNewAgentRuntimeConfig(input?: {
       intervalSec: input?.intervalSec ?? defaultCreateValues.intervalSec,
       wakeOnDemand: true,
       cooldownSec: 10,
-      maxConcurrentRuns: 1,
+      maxConcurrentRuns: AGENT_DEFAULT_MAX_CONCURRENT_RUNS,
     },
   };
 }

ui/src/pages/AgentDetail.tsx

@@ -762,12 +762,13 @@ export function AgentDetail() {
   }, [agent?.companyId, selectedCompanyId, setSelectedCompanyId]);
 
   const agentAction = useMutation({
-    mutationFn: async (action: "invoke" | "pause" | "resume" | "terminate") => {
+    mutationFn: async (action: "invoke" | "pause" | "resume" | "approve" | "terminate") => {
       if (!agentLookupRef) return Promise.reject(new Error("No agent reference"));
       switch (action) {
         case "invoke": return agentsApi.invoke(agentLookupRef, resolvedCompanyId ?? undefined);
         case "pause": return agentsApi.pause(agentLookupRef, resolvedCompanyId ?? undefined);
         case "resume": return agentsApi.resume(agentLookupRef, resolvedCompanyId ?? undefined);
+        case "approve": return agentsApi.approve(agentLookupRef, resolvedCompanyId ?? undefined);
         case "terminate": return agentsApi.terminate(agentLookupRef, resolvedCompanyId ?? undefined);
       }
     },
@@ -1021,9 +1022,18 @@ export function AgentDetail() {
 
       {actionError && <p className="text-sm text-destructive">{actionError}</p>}
       {isPendingApproval && (
-        <p className="text-sm text-amber-500">
-          This agent is pending board approval and cannot be invoked yet.
-        </p>
+        <div className="flex flex-wrap items-center gap-3 rounded-md border border-amber-300/60 bg-amber-50 px-3 py-2 text-sm text-amber-900 dark:border-amber-400/40 dark:bg-amber-950/30 dark:text-amber-200">
+          <span>This agent is pending board approval and cannot be invoked yet.</span>
+          <Button
+            variant="outline"
+            size="sm"
+            onClick={() => agentAction.mutate("approve")}
+            disabled={agentAction.isPending}
+          >
+            <CheckCircle2 className="h-3.5 w-3.5 sm:mr-1" />
+            <span>Approve agent</span>
+          </Button>
+        </div>
       )}
 
       {/* Floating Save/Cancel (desktop) */}

ui/src/pages/Inbox.tsx

@@ -93,6 +93,7 @@ import {
 } from "lucide-react";
 
 const INBOX_HEARTBEAT_RUN_LIMIT = 200;
+const INBOX_ISSUE_LIST_LIMIT = 500;
 import { Input } from "@/components/ui/input";
 import { PageTabBar } from "../components/PageTabBar";
 import type { Approval, HeartbeatRun, Issue, JoinRequest } from "@paperclipai/shared";
@@ -714,9 +715,9 @@ export function Inbox() {
   const isolatedWorkspacesEnabled = experimentalSettings?.enableIsolatedWorkspaces === true;
   const { data: executionWorkspaces = [] } = useQuery({
     queryKey: selectedCompanyId
-      ? queryKeys.executionWorkspaces.list(selectedCompanyId)
+      ? queryKeys.executionWorkspaces.summaryList(selectedCompanyId)
       : ["execution-workspaces", "__disabled__"],
-    queryFn: () => executionWorkspacesApi.list(selectedCompanyId!),
+    queryFn: () => executionWorkspacesApi.listSummaries(selectedCompanyId!),
     enabled: !!selectedCompanyId && isolatedWorkspacesEnabled,
   });
 
@@ -776,7 +777,11 @@ export function Inbox() {
 
   const { data: issues, isLoading: isIssuesLoading } = useQuery({
     queryKey: [...queryKeys.issues.list(selectedCompanyId!), "with-routine-executions"],
-    queryFn: () => issuesApi.list(selectedCompanyId!, { includeRoutineExecutions: true }),
+    queryFn: () =>
+      issuesApi.list(selectedCompanyId!, {
+        includeRoutineExecutions: true,
+        limit: INBOX_ISSUE_LIST_LIMIT,
+      }),
     enabled: !!selectedCompanyId,
   });
   const {
@@ -790,6 +795,7 @@ export function Inbox() {
         inboxArchivedByUserId: "me",
         status: INBOX_MINE_ISSUE_STATUS_FILTER,
         includeRoutineExecutions: true,
+        limit: INBOX_ISSUE_LIST_LIMIT,
       }),
     enabled: !!selectedCompanyId,
   });
@@ -803,6 +809,7 @@ export function Inbox() {
         touchedByUserId: "me",
         status: INBOX_MINE_ISSUE_STATUS_FILTER,
         includeRoutineExecutions: true,
+        limit: INBOX_ISSUE_LIST_LIMIT,
       }),
     enabled: !!selectedCompanyId,
   });
@@ -1937,7 +1944,7 @@ export function Inbox() {
             enableRoutineVisibilityFilter
             buttonVariant="outline"
             iconOnly
-            workspaces={isolatedWorkspacesEnabled ? executionWorkspaces.filter((w) => w.mode === "isolated_workspace" && w.status === "active").map((w) => ({ id: w.id, name: w.name })) : undefined}
+            workspaces={isolatedWorkspacesEnabled ? executionWorkspaces.filter((w) => w.mode === "isolated_workspace").map((w) => ({ id: w.id, name: w.name })) : undefined}
           />
           <Popover>
             <PopoverTrigger asChild>