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[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>
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38 changed files with 1569 additions and 240 deletions
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@ -3,12 +3,15 @@ import os from "node:os";
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import path from "node:path";
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import { execFileSync } from "node:child_process";
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import { randomUUID } from "node:crypto";
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import { eq } from "drizzle-orm";
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import { afterEach, describe, expect, it, vi } from "vitest";
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import {
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agents,
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authUsers,
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companies,
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createDb,
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issueComments,
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issues,
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projects,
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routines,
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routineTriggers,
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@ -17,6 +20,7 @@ import {
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copyGitHooksToWorktreeGitDir,
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copySeededSecretsKey,
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pauseSeededScheduledRoutines,
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quarantineSeededWorktreeExecutionState,
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readSourceAttachmentBody,
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rebindWorkspaceCwd,
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resolveSourceConfigPath,
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@ -282,6 +286,138 @@ describe("worktree helpers", () => {
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expect(full.nullifyColumns).toEqual({});
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});
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itEmbeddedPostgres("quarantines copied live execution state in seeded worktree databases", async () => {
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const tempDb = await startEmbeddedPostgresTestDatabase("paperclip-worktree-quarantine-");
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const db = createDb(tempDb.connectionString);
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const companyId = randomUUID();
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const agentId = randomUUID();
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const idleAgentId = randomUUID();
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const inProgressIssueId = randomUUID();
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const todoIssueId = randomUUID();
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const reviewIssueId = randomUUID();
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const userIssueId = randomUUID();
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try {
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await db.insert(companies).values({
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id: companyId,
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name: "Paperclip",
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issuePrefix: "WTQ",
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requireBoardApprovalForNewAgents: false,
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});
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await db.insert(agents).values([
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{
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id: agentId,
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companyId,
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name: "CodexCoder",
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role: "engineer",
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status: "running",
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adapterType: "codex_local",
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adapterConfig: {},
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runtimeConfig: {
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heartbeat: { enabled: true, intervalSec: 60 },
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wakeOnDemand: true,
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},
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permissions: {},
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},
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{
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id: idleAgentId,
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companyId,
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name: "Reviewer",
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role: "reviewer",
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status: "idle",
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adapterType: "codex_local",
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adapterConfig: {},
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runtimeConfig: { heartbeat: { enabled: false, intervalSec: 300 } },
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permissions: {},
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},
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]);
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await db.insert(issues).values([
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{
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id: inProgressIssueId,
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companyId,
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title: "Copied in-flight issue",
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status: "in_progress",
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priority: "medium",
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assigneeAgentId: agentId,
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issueNumber: 1,
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identifier: "WTQ-1",
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executionAgentNameKey: "codexcoder",
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executionLockedAt: new Date("2026-04-18T00:00:00.000Z"),
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},
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{
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id: todoIssueId,
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companyId,
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title: "Copied assigned todo issue",
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status: "todo",
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priority: "medium",
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assigneeAgentId: agentId,
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issueNumber: 2,
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identifier: "WTQ-2",
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},
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{
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id: reviewIssueId,
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companyId,
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title: "Copied assigned review issue",
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status: "in_review",
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priority: "medium",
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assigneeAgentId: idleAgentId,
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issueNumber: 3,
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identifier: "WTQ-3",
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},
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{
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id: userIssueId,
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companyId,
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title: "Copied user issue",
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status: "todo",
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priority: "medium",
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assigneeUserId: "user-1",
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issueNumber: 4,
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identifier: "WTQ-4",
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},
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]);
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await expect(quarantineSeededWorktreeExecutionState(tempDb.connectionString)).resolves.toEqual({
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disabledTimerHeartbeats: 1,
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resetRunningAgents: 1,
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quarantinedInProgressIssues: 1,
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unassignedTodoIssues: 1,
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unassignedReviewIssues: 1,
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});
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const [quarantinedAgent] = await db.select().from(agents).where(eq(agents.id, agentId));
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expect(quarantinedAgent?.status).toBe("idle");
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expect(quarantinedAgent?.runtimeConfig).toMatchObject({
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heartbeat: { enabled: false, intervalSec: 60 },
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wakeOnDemand: true,
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});
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const [inProgressIssue] = await db.select().from(issues).where(eq(issues.id, inProgressIssueId));
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expect(inProgressIssue?.status).toBe("blocked");
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expect(inProgressIssue?.assigneeAgentId).toBeNull();
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expect(inProgressIssue?.executionAgentNameKey).toBeNull();
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expect(inProgressIssue?.executionLockedAt).toBeNull();
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const [todoIssue] = await db.select().from(issues).where(eq(issues.id, todoIssueId));
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expect(todoIssue?.status).toBe("todo");
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expect(todoIssue?.assigneeAgentId).toBeNull();
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const [reviewIssue] = await db.select().from(issues).where(eq(issues.id, reviewIssueId));
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expect(reviewIssue?.status).toBe("in_review");
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expect(reviewIssue?.assigneeAgentId).toBeNull();
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const [userIssue] = await db.select().from(issues).where(eq(issues.id, userIssueId));
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expect(userIssue?.status).toBe("todo");
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expect(userIssue?.assigneeUserId).toBe("user-1");
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const comments = await db.select().from(issueComments).where(eq(issueComments.issueId, inProgressIssueId));
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expect(comments).toHaveLength(1);
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expect(comments[0]?.body).toContain("Quarantined during worktree seed");
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} finally {
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await db.$client?.end?.({ timeout: 5 }).catch(() => undefined);
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await tempDb.cleanup();
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}
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}, 20_000);
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it("copies the source local_encrypted secrets key into the seeded worktree instance", () => {
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const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-secrets-"));
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const originalInlineMasterKey = process.env.PAPERCLIP_SECRETS_MASTER_KEY;
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