README.md

@@ -177,8 +177,6 @@ Open source. Self-hosted. No Paperclip account required.
 npx paperclipai onboard --yes
 ```
 
-If you already have Paperclip configured, rerunning `onboard` keeps the existing config in place. Use `paperclipai configure` to edit settings.
-
 Or manually:
 
 ```bash

cli/README.md

@@ -1,292 +0,0 @@
-<p align="center">
-  <img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/header.png" alt="Paperclip — runs your business" width="720" />
-</p>
-
-<p align="center">
-  <a href="#quickstart"><strong>Quickstart</strong></a> &middot;
-  <a href="https://paperclip.ing/docs"><strong>Docs</strong></a> &middot;
-  <a href="https://github.com/paperclipai/paperclip"><strong>GitHub</strong></a> &middot;
-  <a href="https://discord.gg/m4HZY7xNG3"><strong>Discord</strong></a>
-</p>
-
-<p align="center">
-  <a href="https://github.com/paperclipai/paperclip/blob/master/LICENSE"><img src="https://img.shields.io/badge/license-MIT-blue" alt="MIT License" /></a>
-  <a href="https://github.com/paperclipai/paperclip/stargazers"><img src="https://img.shields.io/github/stars/paperclipai/paperclip?style=flat" alt="Stars" /></a>
-  <a href="https://discord.gg/m4HZY7xNG3"><img src="https://img.shields.io/discord/000000000?label=discord" alt="Discord" /></a>
-</p>
-
-<br/>
-
-<div align="center">
-  <video src="https://github.com/user-attachments/assets/773bdfb2-6d1e-4e30-8c5f-3487d5b70c8f" width="600" controls></video>
-</div>
-
-<br/>
-
-## What is Paperclip?
-
-# Open-source orchestration for zero-human companies
-
-**If OpenClaw is an _employee_, Paperclip is the _company_**
-
-Paperclip is a Node.js server and React UI that orchestrates a team of AI agents to run a business. Bring your own agents, assign goals, and track your agents' work and costs from one dashboard.
-
-It looks like a task manager — but under the hood it has org charts, budgets, governance, goal alignment, and agent coordination.
-
-**Manage business goals, not pull requests.**
-
-|        | Step            | Example                                                            |
-| ------ | --------------- | ------------------------------------------------------------------ |
-| **01** | Define the goal | _"Build the #1 AI note-taking app to $1M MRR."_                    |
-| **02** | Hire the team   | CEO, CTO, engineers, designers, marketers — any bot, any provider. |
-| **03** | Approve and run | Review strategy. Set budgets. Hit go. Monitor from the dashboard.  |
-
-<br/>
-
-> **COMING SOON: Clipmart** — Download and run entire companies with one click. Browse pre-built company templates — full org structures, agent configs, and skills — and import them into your Paperclip instance in seconds.
-
-<br/>
-
-<div align="center">
-<table>
-  <tr>
-    <td align="center"><strong>Works<br/>with</strong></td>
-    <td align="center"><img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/logos/openclaw.svg" width="32" alt="OpenClaw" /><br/><sub>OpenClaw</sub></td>
-    <td align="center"><img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/logos/claude.svg" width="32" alt="Claude" /><br/><sub>Claude Code</sub></td>
-    <td align="center"><img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/logos/codex.svg" width="32" alt="Codex" /><br/><sub>Codex</sub></td>
-    <td align="center"><img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/logos/cursor.svg" width="32" alt="Cursor" /><br/><sub>Cursor</sub></td>
-    <td align="center"><img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/logos/bash.svg" width="32" alt="Bash" /><br/><sub>Bash</sub></td>
-    <td align="center"><img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/logos/http.svg" width="32" alt="HTTP" /><br/><sub>HTTP</sub></td>
-  </tr>
-</table>
-
-<em>If it can receive a heartbeat, it's hired.</em>
-
-</div>
-
-<br/>
-
-## Paperclip is right for you if
-
-- ✅ You want to build **autonomous AI companies**
-- ✅ You **coordinate many different agents** (OpenClaw, Codex, Claude, Cursor) toward a common goal
-- ✅ You have **20 simultaneous Claude Code terminals** open and lose track of what everyone is doing
-- ✅ You want agents running **autonomously 24/7**, but still want to audit work and chime in when needed
-- ✅ You want to **monitor costs** and enforce budgets
-- ✅ You want a process for managing agents that **feels like using a task manager**
-- ✅ You want to manage your autonomous businesses **from your phone**
-
-<br/>
-
-## Features
-
-<table>
-<tr>
-<td align="center" width="33%">
-<h3>🔌 Bring Your Own Agent</h3>
-Any agent, any runtime, one org chart. If it can receive a heartbeat, it's hired.
-</td>
-<td align="center" width="33%">
-<h3>🎯 Goal Alignment</h3>
-Every task traces back to the company mission. Agents know <em>what</em> to do and <em>why</em>.
-</td>
-<td align="center" width="33%">
-<h3>💓 Heartbeats</h3>
-Agents wake on a schedule, check work, and act. Delegation flows up and down the org chart.
-</td>
-</tr>
-<tr>
-<td align="center">
-<h3>💰 Cost Control</h3>
-Monthly budgets per agent. When they hit the limit, they stop. No runaway costs.
-</td>
-<td align="center">
-<h3>🏢 Multi-Company</h3>
-One deployment, many companies. Complete data isolation. One control plane for your portfolio.
-</td>
-<td align="center">
-<h3>🎫 Ticket System</h3>
-Every conversation traced. Every decision explained. Full tool-call tracing and immutable audit log.
-</td>
-</tr>
-<tr>
-<td align="center">
-<h3>🛡️ Governance</h3>
-You're the board. Approve hires, override strategy, pause or terminate any agent — at any time.
-</td>
-<td align="center">
-<h3>📊 Org Chart</h3>
-Hierarchies, roles, reporting lines. Your agents have a boss, a title, and a job description.
-</td>
-<td align="center">
-<h3>📱 Mobile Ready</h3>
-Monitor and manage your autonomous businesses from anywhere.
-</td>
-</tr>
-</table>
-
-<br/>
-
-## Problems Paperclip solves
-
-| Without Paperclip                                                                                                                     | With Paperclip                                                                                                                         |
-| ------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- |
-| ❌ You have 20 Claude Code tabs open and can't track which one does what. On reboot you lose everything.                              | ✅ Tasks are ticket-based, conversations are threaded, sessions persist across reboots.                                                |
-| ❌ You manually gather context from several places to remind your bot what you're actually doing.                                     | ✅ Context flows from the task up through the project and company goals — your agent always knows what to do and why.                  |
-| ❌ Folders of agent configs are disorganized and you're re-inventing task management, communication, and coordination between agents. | ✅ Paperclip gives you org charts, ticketing, delegation, and governance out of the box — so you run a company, not a pile of scripts. |
-| ❌ Runaway loops waste hundreds of dollars of tokens and max your quota before you even know what happened.                           | ✅ Cost tracking surfaces token budgets and throttles agents when they're out. Management prioritizes with budgets.                    |
-| ❌ You have recurring jobs (customer support, social, reports) and have to remember to manually kick them off.                        | ✅ Heartbeats handle regular work on a schedule. Management supervises.                                                                |
-| ❌ You have an idea, you have to find your repo, fire up Claude Code, keep a tab open, and babysit it.                                | ✅ Add a task in Paperclip. Your coding agent works on it until it's done. Management reviews their work.                              |
-
-<br/>
-
-## Why Paperclip is special
-
-Paperclip handles the hard orchestration details correctly.
-
-|                                   |                                                                                                               |
-| --------------------------------- | ------------------------------------------------------------------------------------------------------------- |
-| **Atomic execution.**             | Task checkout and budget enforcement are atomic, so no double-work and no runaway spend.                      |
-| **Persistent agent state.**       | Agents resume the same task context across heartbeats instead of restarting from scratch.                     |
-| **Runtime skill injection.**      | Agents can learn Paperclip workflows and project context at runtime, without retraining.                      |
-| **Governance with rollback.**     | Approval gates are enforced, config changes are revisioned, and bad changes can be rolled back safely.        |
-| **Goal-aware execution.**         | Tasks carry full goal ancestry so agents consistently see the "why," not just a title.                        |
-| **Portable company templates.**   | Export/import orgs, agents, and skills with secret scrubbing and collision handling.                          |
-| **True multi-company isolation.** | Every entity is company-scoped, so one deployment can run many companies with separate data and audit trails. |
-
-<br/>
-
-## What Paperclip is not
-
-|                              |                                                                                                                      |
-| ---------------------------- | -------------------------------------------------------------------------------------------------------------------- |
-| **Not a chatbot.**           | Agents have jobs, not chat windows.                                                                                  |
-| **Not an agent framework.**  | We don't tell you how to build agents. We tell you how to run a company made of them.                                |
-| **Not a workflow builder.**  | No drag-and-drop pipelines. Paperclip models companies — with org charts, goals, budgets, and governance.            |
-| **Not a prompt manager.**    | Agents bring their own prompts, models, and runtimes. Paperclip manages the organization they work in.               |
-| **Not a single-agent tool.** | This is for teams. If you have one agent, you probably don't need Paperclip. If you have twenty — you definitely do. |
-| **Not a code review tool.**  | Paperclip orchestrates work, not pull requests. Bring your own review process.                                       |
-
-<br/>
-
-## Quickstart
-
-Open source. Self-hosted. No Paperclip account required.
-
-```bash
-npx paperclipai onboard --yes
-```
-
-If you already have Paperclip configured, rerunning `onboard` keeps the existing config in place. Use `paperclipai configure` to edit settings.
-
-Or manually:
-
-```bash
-git clone https://github.com/paperclipai/paperclip.git
-cd paperclip
-pnpm install
-pnpm dev
-```
-
-This starts the API server at `http://localhost:3100`. An embedded PostgreSQL database is created automatically — no setup required.
-
-> **Requirements:** Node.js 20+, pnpm 9.15+
-
-<br/>
-
-## FAQ
-
-**What does a typical setup look like?**
-Locally, a single Node.js process manages an embedded Postgres and local file storage. For production, point it at your own Postgres and deploy however you like. Configure projects, agents, and goals — the agents take care of the rest.
-
-If you're a solo-entreprenuer you can use Tailscale to access Paperclip on the go. Then later you can deploy to e.g. Vercel when you need it.
-
-**Can I run multiple companies?**
-Yes. A single deployment can run an unlimited number of companies with complete data isolation.
-
-**How is Paperclip different from agents like OpenClaw or Claude Code?**
-Paperclip _uses_ those agents. It orchestrates them into a company — with org charts, budgets, goals, governance, and accountability.
-
-**Why should I use Paperclip instead of just pointing my OpenClaw to Asana or Trello?**
-Agent orchestration has subtleties in how you coordinate who has work checked out, how to maintain sessions, monitoring costs, establishing governance - Paperclip does this for you.
-
-(Bring-your-own-ticket-system is on the Roadmap)
-
-**Do agents run continuously?**
-By default, agents run on scheduled heartbeats and event-based triggers (task assignment, @-mentions). You can also hook in continuous agents like OpenClaw. You bring your agent and Paperclip coordinates.
-
-<br/>
-
-## Development
-
-```bash
-pnpm dev              # Full dev (API + UI, watch mode)
-pnpm dev:once         # Full dev without file watching
-pnpm dev:server       # Server only
-pnpm build            # Build all
-pnpm typecheck        # Type checking
-pnpm test:run         # Run tests
-pnpm db:generate      # Generate DB migration
-pnpm db:migrate       # Apply migrations
-```
-
-See [doc/DEVELOPING.md](https://github.com/paperclipai/paperclip/blob/master/doc/DEVELOPING.md) for the full development guide.
-
-<br/>
-
-## Roadmap
-
-- ✅ Plugin system (e.g. add a knowledge base, custom tracing, queues, etc)
-- ✅ Get OpenClaw / claw-style agent employees
-- ✅ companies.sh - import and export entire organizations
-- ✅ Easy AGENTS.md configurations
-- ✅ Skills Manager
-- ✅ Scheduled Routines
-- ✅ Better Budgeting
-- ⚪ Artifacts & Deployments
-- ⚪ CEO Chat
-- ⚪ MAXIMIZER MODE
-- ⚪ Multiple Human Users
-- ⚪ Cloud / Sandbox agents (e.g. Cursor / e2b agents)
-- ⚪ Cloud deployments
-- ⚪ Desktop App
-
-<br/>
-
-## Community & Plugins
-
-Find Plugins and more at [awesome-paperclip](https://github.com/gsxdsm/awesome-paperclip)
-
-## Contributing
-
-We welcome contributions. See the [contributing guide](https://github.com/paperclipai/paperclip/blob/master/CONTRIBUTING.md) for details.
-
-<br/>
-
-## Community
-
-- [Discord](https://discord.gg/m4HZY7xNG3) — Join the community
-- [GitHub Issues](https://github.com/paperclipai/paperclip/issues) — bugs and feature requests
-- [GitHub Discussions](https://github.com/paperclipai/paperclip/discussions) — ideas and RFC
-
-<br/>
-
-## License
-
-MIT &copy; 2026 Paperclip
-
-## Star History
-
-[![Star History Chart](https://api.star-history.com/image?repos=paperclipai/paperclip&type=date&legend=top-left)](https://www.star-history.com/?repos=paperclipai%2Fpaperclip&type=date&legend=top-left)
-
-<br/>
-
----
-
-<p align="center">
-  <img src="https://raw.githubusercontent.com/paperclipai/paperclip/master/doc/assets/footer.jpg" alt="" width="720" />
-</p>
-
-<p align="center">
-  <sub>Open source under MIT. Built for people who want to run companies, not babysit agents.</sub>
-</p>

cli/src/__tests__/onboard.test.ts

@@ -1,105 +0,0 @@
-import fs from "node:fs";
-import os from "node:os";
-import path from "node:path";
-import { afterEach, beforeEach, describe, expect, it } from "vitest";
-import { onboard } from "../commands/onboard.js";
-import type { PaperclipConfig } from "../config/schema.js";
-
-const ORIGINAL_ENV = { ...process.env };
-
-function createExistingConfigFixture() {
-  const root = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-onboard-"));
-  const runtimeRoot = path.join(root, "runtime");
-  const configPath = path.join(root, ".paperclip", "config.json");
-  const config: PaperclipConfig = {
-    $meta: {
-      version: 1,
-      updatedAt: "2026-03-29T00:00:00.000Z",
-      source: "configure",
-    },
-    database: {
-      mode: "embedded-postgres",
-      embeddedPostgresDataDir: path.join(runtimeRoot, "db"),
-      embeddedPostgresPort: 54329,
-      backup: {
-        enabled: true,
-        intervalMinutes: 60,
-        retentionDays: 30,
-        dir: path.join(runtimeRoot, "backups"),
-      },
-    },
-    logging: {
-      mode: "file",
-      logDir: path.join(runtimeRoot, "logs"),
-    },
-    server: {
-      deploymentMode: "local_trusted",
-      exposure: "private",
-      host: "127.0.0.1",
-      port: 3100,
-      allowedHostnames: [],
-      serveUi: true,
-    },
-    auth: {
-      baseUrlMode: "auto",
-      disableSignUp: false,
-    },
-    storage: {
-      provider: "local_disk",
-      localDisk: {
-        baseDir: path.join(runtimeRoot, "storage"),
-      },
-      s3: {
-        bucket: "paperclip",
-        region: "us-east-1",
-        prefix: "",
-        forcePathStyle: false,
-      },
-    },
-    secrets: {
-      provider: "local_encrypted",
-      strictMode: false,
-      localEncrypted: {
-        keyFilePath: path.join(runtimeRoot, "secrets", "master.key"),
-      },
-    },
-  };
-
-  fs.mkdirSync(path.dirname(configPath), { recursive: true });
-  fs.writeFileSync(configPath, `${JSON.stringify(config, null, 2)}\n`, { mode: 0o600 });
-
-  return { configPath, configText: fs.readFileSync(configPath, "utf8") };
-}
-
-describe("onboard", () => {
-  beforeEach(() => {
-    process.env = { ...ORIGINAL_ENV };
-    delete process.env.PAPERCLIP_AGENT_JWT_SECRET;
-    delete process.env.PAPERCLIP_SECRETS_MASTER_KEY;
-    delete process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
-  });
-
-  afterEach(() => {
-    process.env = { ...ORIGINAL_ENV };
-  });
-
-  it("preserves an existing config when rerun without flags", async () => {
-    const fixture = createExistingConfigFixture();
-
-    await onboard({ config: fixture.configPath });
-
-    expect(fs.readFileSync(fixture.configPath, "utf8")).toBe(fixture.configText);
-    expect(fs.existsSync(`${fixture.configPath}.backup`)).toBe(false);
-    expect(fs.existsSync(path.join(path.dirname(fixture.configPath), ".env"))).toBe(true);
-  });
-
-  it("preserves an existing config when rerun with --yes", async () => {
-    const fixture = createExistingConfigFixture();
-
-    await onboard({ config: fixture.configPath, yes: true, invokedByRun: true });
-
-    expect(fs.readFileSync(fixture.configPath, "utf8")).toBe(fixture.configText);
-    expect(fs.existsSync(`${fixture.configPath}.backup`)).toBe(false);
-    expect(fs.existsSync(path.join(path.dirname(fixture.configPath), ".env"))).toBe(true);
-  });
-});

cli/src/commands/onboard.ts

@@ -244,12 +244,11 @@ export async function onboard(opts: OnboardOptions): Promise<void> {
     ),
   );
 
-  let existingConfig: PaperclipConfig | null = null;
   if (configExists(opts.config)) {
-    p.log.message(pc.dim(`${configPath} exists`));
+    p.log.message(pc.dim(`${configPath} exists, updating config`));
 
     try {
-      existingConfig = readConfig(opts.config);
+      readConfig(opts.config);
     } catch (err) {
       p.log.message(
         pc.yellow(
@@ -259,76 +258,6 @@ export async function onboard(opts: OnboardOptions): Promise<void> {
     }
   }
 
-  if (existingConfig) {
-    p.log.message(
-      pc.dim("Existing Paperclip install detected; keeping the current configuration unchanged."),
-    );
-    p.log.message(pc.dim(`Use ${pc.cyan("paperclipai configure")} if you want to change settings.`));
-
-    const jwtSecret = ensureAgentJwtSecret(configPath);
-    const envFilePath = resolveAgentJwtEnvFile(configPath);
-    if (jwtSecret.created) {
-      p.log.success(`Created ${pc.cyan("PAPERCLIP_AGENT_JWT_SECRET")} in ${pc.dim(envFilePath)}`);
-    } else if (process.env.PAPERCLIP_AGENT_JWT_SECRET?.trim()) {
-      p.log.info(`Using existing ${pc.cyan("PAPERCLIP_AGENT_JWT_SECRET")} from environment`);
-    } else {
-      p.log.info(`Using existing ${pc.cyan("PAPERCLIP_AGENT_JWT_SECRET")} in ${pc.dim(envFilePath)}`);
-    }
-
-    const keyResult = ensureLocalSecretsKeyFile(existingConfig, configPath);
-    if (keyResult.status === "created") {
-      p.log.success(`Created local secrets key file at ${pc.dim(keyResult.path)}`);
-    } else if (keyResult.status === "existing") {
-      p.log.message(pc.dim(`Using existing local secrets key file at ${keyResult.path}`));
-    }
-
-    p.note(
-      [
-        "Existing config preserved",
-        `Database: ${existingConfig.database.mode}`,
-        existingConfig.llm ? `LLM: ${existingConfig.llm.provider}` : "LLM: not configured",
-        `Logging: ${existingConfig.logging.mode} -> ${existingConfig.logging.logDir}`,
-        `Server: ${existingConfig.server.deploymentMode}/${existingConfig.server.exposure} @ ${existingConfig.server.host}:${existingConfig.server.port}`,
-        `Allowed hosts: ${existingConfig.server.allowedHostnames.length > 0 ? existingConfig.server.allowedHostnames.join(", ") : "(loopback only)"}`,
-        `Auth URL mode: ${existingConfig.auth.baseUrlMode}${existingConfig.auth.publicBaseUrl ? ` (${existingConfig.auth.publicBaseUrl})` : ""}`,
-        `Storage: ${existingConfig.storage.provider}`,
-        `Secrets: ${existingConfig.secrets.provider} (strict mode ${existingConfig.secrets.strictMode ? "on" : "off"})`,
-        "Agent auth: PAPERCLIP_AGENT_JWT_SECRET configured",
-      ].join("\n"),
-      "Configuration ready",
-    );
-
-    p.note(
-      [
-        `Run: ${pc.cyan("paperclipai run")}`,
-        `Reconfigure later: ${pc.cyan("paperclipai configure")}`,
-        `Diagnose setup: ${pc.cyan("paperclipai doctor")}`,
-      ].join("\n"),
-      "Next commands",
-    );
-
-    let shouldRunNow = opts.run === true || opts.yes === true;
-    if (!shouldRunNow && !opts.invokedByRun && process.stdin.isTTY && process.stdout.isTTY) {
-      const answer = await p.confirm({
-        message: "Start Paperclip now?",
-        initialValue: true,
-      });
-      if (!p.isCancel(answer)) {
-        shouldRunNow = answer;
-      }
-    }
-
-    if (shouldRunNow && !opts.invokedByRun) {
-      process.env.PAPERCLIP_OPEN_ON_LISTEN = "true";
-      const { runCommand } = await import("./run.js");
-      await runCommand({ config: configPath, repair: true, yes: true });
-      return;
-    }
-
-    p.outro("Existing Paperclip setup is ready.");
-    return;
-  }
-
   let setupMode: SetupMode = "quickstart";
   if (opts.yes) {
     p.log.message(pc.dim("`--yes` enabled: using Quickstart defaults."));

docs/cli/setup-commands.md

@@ -33,8 +33,6 @@ Interactive first-time setup:
 pnpm paperclipai onboard
 ```
 
-If Paperclip is already configured, rerunning `onboard` keeps the existing config in place. Use `paperclipai configure` to change settings on an existing install.
-
 First prompt:
 
 1. `Quickstart` (recommended): local defaults (embedded database, no LLM provider, local disk storage, default secrets)
@@ -52,8 +50,6 @@ Non-interactive defaults + immediate start (opens browser on server listen):
 pnpm paperclipai onboard --yes
 ```
 
-On an existing install, `--yes` now preserves the current config and just starts Paperclip with that setup.
-
 ## `paperclipai doctor`
 
 Health checks with optional auto-repair:

docs/start/quickstart.md

@@ -13,8 +13,6 @@ npx paperclipai onboard --yes
 
 This walks you through setup, configures your environment, and gets Paperclip running.
 
-If you already have a Paperclip install, rerunning `onboard` keeps your current config and data paths intact. Use `paperclipai configure` if you want to edit settings.
-
 To start Paperclip again later:
 
 ```sh

package.json

@@ -16,7 +16,7 @@
     "db:migrate": "pnpm --filter @paperclipai/db migrate",
     "secrets:migrate-inline-env": "tsx scripts/migrate-inline-env-secrets.ts",
     "db:backup": "./scripts/backup-db.sh",
-    "paperclipai": "tsx cli/src/index.ts",
+    "paperclipai": "node cli/node_modules/tsx/dist/cli.mjs cli/src/index.ts",
     "build:npm": "./scripts/build-npm.sh",
     "release": "./scripts/release.sh",
     "release:canary": "./scripts/release.sh canary",